| JAPANESE | ENGLISH |

*Image Processing Research Team, Center for Advanced Photonics, RIKEN*

# Publication and Presentation List

### International Journal Papers:

2020 2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004### International Conference Papers (Refereed Paper):

2019 2018 2017 2016 2014 2013 2012 2010 2009 2008 2007 2003### International Invited Talks, Conferences, Symposiums, and Workshops:

2019 2018 2017 2016 2015 2014 2013 2012 2011 2010 2009 2008 2007 2006 2005 2004

### International Journal Papers

- 2020:
- T. Kitrungrotsakul, X.-X Han, Y. Iwamoto, S. Takemoto, H. Yokota, S. Ipponjima, T. Nemoto, X. Wei, and Y.-W. Chen, "An end-to-end CNN and LSTM network with 3D anchors for mitotic cell detection in 4D microscopic images and its parallel implementation on multiple GPUs", Neural Computing and Applications, Vol. 32, pp. 5669–5679, 2020.
- K. Omodaka, S. Fujioka, G. An, T. Udagawa, S. Tsuda, Y. Shiga, S. Morishita, T. Kikawa, K. Pak, M. Akiba, H. Yokota, and T. Nakazawa, “Structural Characterization of Glaucoma Patients with Low Ocular Blood Flow”, Current Eye Research, 2020.

- 2019:
- T. Kitrungrotsakul, X.-X Han, Y. Iwamoto, S. Takemoto, H. Yokota, S. Ipponjima, T. Nemoto, X. Wei, and Y.-W. Chen, "A Cascade of 2.5D CNN and Bidirectional CLSTM Network for Mitotic Cell Detection in 4D Microscopy Image", IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2019.
- S. Inagaki, M. Agetsuma, S. Ohara, T. Iijima, H. Yokota, T. Wazawa, Y. Arai, and T. Nagai, “Imaging local brain activity of multiple freely moving mice sharing the same environment”, Scientific Reports, Vol 9, pp. 7460:1-9, 2019.
- S. Takagi, S. Kudo, H. Yokota, M. Akiba, M. Mandai, Y. Hirami, M. Takahashi, Y. Kurimoto, and M. Ishida, “Assessment of the deformation of the outer nuclear layer in the Epiretinal membrane using spectral-domain optical coherence tomography”, BMC Ophthalmology, Vol. 19, pp. 113:1-7, 2019.
- S. Goto, H. Oka, K. Ayabe, H. Yabushita, M. Nakayama, T. Hasebe, H. Yokota, S. Takagi, M. Sano, and A. Tomita, S. Goto, “Prediction of binding characteristics between von Willebrand factor and platelet glycoprotein Ibα with various mutations by molecular dynamic simulation”, Thrombosis Research, Vol. 184, pp. 129-135, 2019.
- N. Motozawa, G. An, S. Takagi, S. Kitahata, M. Mandai, Y. Hirami, H. Yokota, M. Akiba, A. Tsujikawa, M. Takahashi, and Y. Kurimoto, “Optical Coherence Tomography-Based Deep-Learning Models for Classifying Normal and Age-Related Macular Degeneration and Exudative and Non-Exudative Age-Related Macular Degeneration Changes”, Ophthalmology and Therapy, Vol. 8, pp. 527–539, 2019.
- T. Sera, H. Kuninaga, K. Fukasaku, H. Yokota, and M. Tanaka, “The effectiveness of an averaged airway model in predicting the airflow and particle transport through the airway”, Journal of Aerosol Medicine and Pulmonary Drug Delivery, Vol. 32, No. 5, pp. 278-292, 2019.
- S. Kimura, T. Sakamoto, T. Sera, H. Yokota, K. Ono, D. Doorly, R. Schroter, and G. Tanaka, “Voxel-based modeling of airflow in the human nasal cavity”, Computer Methods in Biomechanics and Biomedical Engineering, vol. 22, No. 3, pp. 331-339, 2019.
- R. Hu, V. Monebhurrun, R. Himeno, H. Yokota, and F. Costen, "A Statistical Parsimony Method for Uncertainty Quantification of FDTD Computation Based on the PCA and Ridge Regression", IEEE Transactions on Antennas and Propagation, vol. 67, no. 7, pp. 4726-4737, 2019.
- R. Sakaguchi, T. Shiraiwa, P. Chivavibul, T. Kasuya, M. Enoki, N. Yamashita, H. Yokota, Y. Matsui, A. Kazama, K. Ozaki, and H. Takamatsu, "Multiscale Analysis of MnS Inclusion Distributions in High Strength Steel", ISIJ International, 2019.
- M. Morita, K. Shimokawa, M. Nishimura, S. Nakamura, Y. Tsujimura, S. Takemoto, T. Tawara, H. Yokota, S. Wemler, D. Miyamoto, H. Ikeno, A. Sato, T. Furuichi, N. Kobayashi, Y. Okumura, Y. Yamaguchi, Y. Okamura-Oho, "ViBrism DB: an interactive search and viewer platform for 2D/3D anatomical images of gene expression and co-expression networks", Nucleic Acids Research, Vol. 47, issue D1, pp. D859-D866, 2019.
- G. An, K. Omodaka, K. Hashimoto, S. Tsuda, Y. Shiga, N. Takada, T. Kikawa, H. Yokota, M. Akiba, T. Nakazawa, “Glaucoma Diagnosis with Machine Learning Based on Optical Coherence Tomography and Color Fundus Images”, Journal of Healthcare Engineering, Vol. 2019, pp. 4061313:1-9, 2019.

- 2018:
- R. Togashi, H. Tanaka, S. Nakamura, H. Yokota, K.Tange, Y. Nakai, H. Yoshioka, H. Hatarhima, H. Akita, "A hepatic pDNA delivery system based on an intracellular environment sensitive vitamin E-scaffold lipid-like material with the aid of an anti-inflammatory drug", Journal of Controlled Release, Vol. 279(10): 262-270, 2018.
- G. An, K. Omodaka, S. Tsuda, Y. Shiga, N. Takada, T. Kikawa, T. Nakazawa, H. Yokota, and M. Akiba, "Comparison of Machine-Learning Classification Models for Glaucoma Management", Journal of Healthcare Engineering, Vol. 2018, Article ID 6874765, 2018.
- B. Abdulkareem, J.-P. Berenger, F. Costen, R. Himeno, and H. Yokota, "An Operator Absorbing Boundary Condition for the Absorption of Electromagnetic Waves in Dispersive Media", IEEE Transactions on Antennas and Propagation, Vol. 66(4): 2147-2150, 2018.
- R. Hu, V. Monebhurrn, R. Himeno, H. Yokota, F. Costen, "An Adaptive Least Angle Regression Method for Uncertainty Quantification in FDTD Computation", IEEE Transactions on Antennas and Propagation, vol. 66(12): 7188-7197, 2018.
- A. Sakane, S. Yoshizawa, H. Yokota, and T. Sasaki, "Dancing Styles of Collective Cell Migration: Image-Based Computational Analysis of JRAB/MICAL-L2", Frontiers in Cell and Developmental Biology, Vol. 6, Article 4: 1-7, 2018.
- T. Sera, S. Komine, M. Arai, Y. Sunaga, H. Yokota, and S. Kudo, “Three-dimensional model of intracellular and intercellular Ca2+ waves propagation in endothelial cells”, Biochemical and Biophysical Research Communications, Vol. 505, Issue 3, pp. 781-786, 2018.
- K. Hori, H. Ikematsu, K. Shinmura, Y. Yoda, Y. Oono, S. Takemoto, H. Yokota, T. Yano, “The Diagnostic Artificial Intelligence (AI) System for Detection of Colon Polyps with High Efficiency of Deep Learning”, Gastrointestinal Endoscopy, Vol. 87, Issue 6, pp. AB:240-241, 2018.

- 2017:
- D. Bashkirova, S. Yoshizawa, R. Latypov, and H. Yokota, "Fast L1 Gauss Transforms for Edge-Aware Image Filtering", Proceedings of the Institute for System Programming of the Russian Academy of Sciences, Vol. 29(4): 55-72, 2017.
- Y. Mimura, S. Takemoto, T. Tachibana, Y. Ogawa, M. Nishimura, H. Yokota, and N. Imamoto, "A statistical image analysis framework for pore-free islands derived from heterogeneity distribution of nuclear pore complexes", Scientific Reports, Vol. 7, Article number: 16315, 2017.
- H. Saito, H. Nishizumi, S. Suzuki, H. Matsumoto, N. Ieki, T. Abe, H. Kiyonari, M. Morita, H. Yokota, N. Hirayama, T. Yamazaki, T. Kikusui, K. Mori, and H. Sakano, "Immobility responses are induced by photoactivation of single glomerular species responsive to fox odour TMT", Nature Communications, Vol. 8, Article number: 16011, 2017.
- V. Odedo, M. Yavuz, F. Costen, R. Himeno, and H. Yokota, "Time Reversal Technique based on Spatio-Temporal Windows for Through the Wall Imaging", IEEE Transactions on Antennas and Propagation Vol. 65(6): 3065–3072, 2017.
- A. M. Abduljabbar, M. E. Yavuz, F. Costen, R. Himeno, and H. Yokota, "Continuous Wavelet Transform-Based Frequency Dispersion Compensation Method for Electromagnetic Time-Reversal Imaging", IEEE Transactions on Antennas and Propagation, Vol. 65(3): 1321-1329, 2017.
- Y.-H. Chang, H. Yokota, K. Abe, C.-T. Tang, and M.-D. Tasi, "Automated Detection and Tracking of Cell Clusters in Time-Lapse Fluorescence Microscopy Images", Journal of Medical and Biological Engineering, Vol. 37(1): 18–25, 2017.
- K. Tekbas, F. Costen, J.-P. Berenger, R. Himeno, and H. Yokota, "Subcell Modeling of Frequency-Dependent Thin Layers in the FDTD Method", IEEE Transactions on Antennas and Propagation, Vol. 65(1): 269-277, 2017.
- K. Omodaka, G. An, S. Tsuda, Y. Shiga, N. Takada, T. Kikawa, H. Takahashi, H. Yokota, M. Akiba, and T. Nakazawa, "Classification of optic disc shape in glaucoma using machine learning based on quantified ocular parameters", PLoS One, Vol. 12(12): 1-10, 2017.
- N. Furushiro, H. Yokota, S. Nakamura, K. Fujisaki, Y. Yamagata, M. Kokubo, R. Himeno, A. Makinouchi, and T. Higuchi, "Three-Dimensional Observation of Microstructure of Bone Tissue Using High-Precision Machining", International Journal of Automation Technology, Vol. 11(6): 883-894, 2017.

- 2016:
- A. Sakane, S. Yoshizawa, M. Nishimura, Y. Tsuchiya, N. Matsushita, K. Miyake, K. Horikawa, I. Imoto, C. Mizuguchi, H. Saito, T. Ueno, S. Matsushita, H. Haga, S. Deguchi, K. Mizuguchi, H. Yokota, and T. Sasaki, "Conformational plasticity of JRAB/MICAL-L2 provides “law and order” in collective cell migration", Molecular Biology of The Cell, Vol. 27(20):3095-3108, 2016.
- A. M. Abduljabbar, M. E. Yavuz, F. Costen, R. Himeno, and H. Yokota, "Frequency Dispersion Compensation Through Variable Window Utilization in Time-Reversal Techniques for Electromagnetic Waves", IEEE Transactions on Antennas and Propagation, vol. 64(8):3636-3639, 2016.
- B. Abdulkareem, J.-P. Berenger, R. Himeno, and H. Yokota, "Huygens Excitation for Biomedical Applications of the FDTD Method", IEEE Transactions on Antennas and Propagation, vol. 64(8):3632-3635, 2016.

- 2015:
- N. Yamashita, M. Morita, W. R. Legant, B.-C. Chen, E. Betzig, H. Yokota, and Y. Mimori-Kiyosue, "Three-dimensional tracking of plus-tips by lattice light-sheet microscopy permits the quantification of microtubule growth trajectories within the mitotic apparatus", Journal of Biomedical Optics, Vol. 20(10):101206:1-18, 2015.
- M. Ono, H. Akuzawa, Y. Nambo, Y. Hirano, J. Kimura, S. Takemoto, S. Nakamura, H.Yokota, R. Himeno, T Higuchi, T. Ohtaki, and S. Tsumagari, "Analysis of the equine ovarian structure during the first twelve months of life by three-dimensional internal structure microscopy", Journal of Veterinary Medical Science, jvms.14-0539, 2015.
- T. Sera, K. Uesugi, N. Yagi, and H. Yokota, "Numerical simulation of airflow and microparticle deposition in a synchrotron micro-CT-based pulmonary acinus model", Computer Methods in Biomechanics and Biomedical Engineering, Vol. 18(13), pp. 1427-1435, 2015.
- K. Isobe, Y. Kimura, S. Kimura, T. Sera, H. Yokota, K. Ono, and G. Tanaka, "Effectiveness of Two-dimensional Medical Image Interpolation in the Transverse Plane in the Voxel Analysis of Nasal Air Flow and Temperature", Transactions of Japanese Society for Medical and Biological Engineering, Vol. 53(3), pp. 160-167, 2015.
- T. Matsumoto, N. Tabata, H. Tamaki, T. Shibasaki, S. Seino, Y. Sunaga, H. Yokota, and M. Fukushima, "Simulation Model of Insulin Granule Dynamics in Pancreatic Beta Cell", IEEJ Transactions on Electronics Information and Systems, Vol. 135(8), pp. 963-970, 2015.
- H. Li, H. Ohta, Y. Tahara, S. Nakamura, K. Taguchi, M. Nakagawa, Y. Oishi, Y. Goto, K. Wada, M. Kaga, M. Inagaki, M. Otagiri, H. Yokota, S. Shibata, H. Sakai, K. Okamura, and N. Yaegashi, "Artificial oxygen carriers rescue placental hypoxia and improve fetal development in the rat pre-eclampsia model", Scientific Reports, Vol. 5:15271, 2015.
- N. Masaki, I. Ishizaki, T. Hayasaka, G. Fisher, N. Sanada, H. Yokota, and M. Setou, "Three-Dimensional Image of Cleavage Bodies in Nuclei Is Configured Using Gas Cluster Ion Beam with Time-of-Flight Secondary Ion Mass Spectrometry", Scientific Reports, 5:10000, 2015.
- T. Ijiri, T. Ashihara, N. Umetani, Y. Koyama, T. Igarashi, R. Haraguchi, H. Yokota, and K. Nakazawa, "Visual Simulation of Cardiac Beating Motion with Shape Matching Dynamics", Transactions of Japanese Society for Medical and Biological Engineering, Vol. 53(3), pp. 130-137, 2015.
- T. Oda, T. Hisano, D. Hay, R. Kinugasa, N. Yamamura, T. Komatsu, H. Yokota, and S. Takagi, "Anatomical Geometry and Thickness of Aponeuroses in Human Cadaver Triceps Surae Muscles", Advanced Biomedical Engineering, Vol. 4, pp.12-15, 2015.

- 2014:
- T. Ijiri, S. Yoshizawa, H. Yokota, and T. Igarashi, "Flower Modeling via X-ray Computed Tomography", ACM Transactions on Graphics, Vol. 33(4):48:1-10, (Proc. of SIGGRAPH'14), 2014.
- Y. Okamura-Oho, K. Shimokawa, M. Nishimura, S. Takemoto, A. Sato, T. Furuichi, and H. Yokota, "Broad Integration of Expression Maps and Co-Expression Networks Compassing Novel Gene Functions in the Brain", Scientific Reports, Vol. 4, 6969:1-11, 2014.
- M. Morita, T. Tawara, M. Nishimura, S. Yoshizawa, B. Chou, I. Kuroki, T. Ijiri, Y. Tsujimura, R. Himeno, and H. Yokota, "Communication Platform for Image Analysis and Sharing in Biology", International Journal of Networking and Computing, Vol. 4, No. 2, pp. 369-391, 2014.
- D. Ueno, K. Makiyama, H. Yamanaka, T. Ijiri, H. Yokota, and Y. Kubota, "Prediction of open urinary tract in laparoscopic partial nephrectomy by virtual resection plane visualization", BMC Urology, Vol. 14(1):47, 2014.
- E. A. Susaki, K. Tainaka, D. Perrin, F. Kishino, T. Tawara, T. M. Watanabe, C. Yokoyama, H. Onoe, M. Eguchi, S. Yamaguchi, T. Abe, H. Kiyonari, Y. Shimizu, A. Miyawaki, H. Yokota, and H. R. Ueda, "Whole-Brain Imaging with Single-Cell Resolution Using Chemical Cocktails and Computational Analysis", Cell, Vol. 157(3), pp. 726-739, 2014.
- E. Chikayama, Y. Sunaga, S. Noda, and H. Yokota, "Solvable model for chemical oscillations", Journal of Mathematical Chemistry, Vol. 52(2), pp. 399-406, 2014.
- T. Hemmi, F. Costen, S. Garcia, R. Himeno, H. Yokota, and M. Mustafa, "Efficient Parallel LOD-FDTD Method for Debye-Dispersive Media", IEEE Transactions on Antennas and Propagation, Vol. 62(3), pp. 1330-1338, 2014.

- 2013:
- S. Yoshizawa and A. Belyaev, "Möbius-invariant curve and surface energies and their applications", Science China Information Sciences, Vol. 56(9), pp. 1-10, 2013.
- T. Ijiri, S. Yoshizawa, Y. Sato, M. Ito, and H. Yokota, "Bilateral Hermite Radial Basis Functions for Contour-based Volume Segmentation", Computer Graphics Forum: The International Journal of Eurographics Association (Proc. of EUROGRAPHICS), Vo. 32(2), pp. 123-132, 2013.
- T. Sera, H. Yokota, R. Himeno, and G. Tanaka, "Gas dispersion of oscillatory flow in expanding and contracting multi-branching airways", International Journal of Heat and Mass Transfer, Vol. 65, pp. 627–634, 2013.
- T. Sera, H. Yokota, G. Tanaka, K. Uesugi, N. Yagi, and R. C. Schroter, "Murine pulmonary acinar mechanics during quasi-static inflation using synchrotron refraction-enhanced computed tomography", Journal of Applied Physiology, Vol. 115(2), pp. 219-228, 2013.
- Y. Nagai, Y. Ohtake, H. Yokota, and H. Suzuki, "Boundary-representable partition of unity for image magnification", Science China Information Sciences, 56(11), pp. 1-12, 2013.

- 2012:
- S. Yoshizawa, A. Belyaev, and H. Yokota, "Shape and Image Interrogation with Curvature Extremalities", Journal for Geometry and Graphics, Vo. 16(1), pp. 81-95, 2012.
- M. Abalenkovs, F, Costen, J.-P. Berender, R. Himeno, H. Yokota, and M. Fujii, "Huygens Subgridding for 3D Frequency-Dependent Finite-Difference Time-Domain Method", IEEE Trans. on Antennas and Propagation, Vol. 60(9), pp. 4336-4344, 2012.
- K. Fujisaki, N. Yamashita, and H. Yokota, "An automated three-dimensional internal structure observation system based on high-speed serial sectioning of steel materials", Precision Engineering, Vo. 36(2), pp. 315-321, 2012.
- S. Hihara, C.-G. Pack, K. Kaizu, T. Tani, T. Hanafusa, T. Nozaki, S. Takemoto, T. Yoshimi, H. Yokota, N. Imamoto, Y. Sako, M. Kinjo, K. Takahashi, T. Nagai, K. Maeshima, "Local Nucleosome Dynamics Facilitate Chromatin Accessibility in Living Mammalian Cells", Cell Reports, Vol. 2(6), pp. 1645-1656, 2012.
- T. Ijiri, T. Ashihara, N. Umetani, T. Igarashi, R. Haraguchi, and H. Yokota, "A Kinematic Approach for Efficient and Robust Simulation of the Cardiac Beating Motion", PLoS One, Vol. 7(5), pp. e36706:1-9, 2012.
- Y. Oho, K. Shimokawa, S. Takemoto, A. Hirakiyama, S. Nakamura, Y. Tsujimura, M. Nishimura, T. Kasukawa, K. Masumoto, I. Nikaido, Y. Shigeyoshi, H. Ueda, G. Song, J. Gee, R. Himeno, and H. Yokota, "Transcriptome tomography for brain analysis in the web-accessible anatomical space", PLoS One, Vol. 7(9), e45373:1-10, 2012.
- K. Kominami, T. Nagai, T. Sawasaki, Y. Tsujimura, K. Yashima, Y. Sunaga, M. Tsuchimochi, J. Nishimura, K. Chiba, J. Nakabayashi, K. Koyamada, Y. Endo, H. Yokota, A. Miyawaki, N. Manabe, and K. Sakamaki, "In Vivo Imaging of Hierarchical Spatiotemporal Activation of Caspase-8 during Apoptosis", PLoS One, Vol. 7(11), e50218:1-18, 2012.
- T. Sera, H. Yokota, K. Uesugi, and N. Yagi, "Airway distension during lung inflation in healthy and allergic-sensitised mice in vivo", Respir. Physiol. Neurobiol., Vol. 185(3), pp. 639-646, 2012.
- K. Kominami, J. Nakabayashi, T. Nagai, Y. Tsujimura, K. Chiba, H. Kimura, A. Miyawaki, T. Sawasaki, H. Yokota, N. Manabe, and K. Sakamaki, "The molecular mechanism of apoptosis upon caspase-8 activation: quantitative experimental validation of a mathematical model", Biochim. Biophys. Acta, Vol. 1823(10), pp. 1825-1840, 2012.

- 2011:
- K. Fujisaki, H. Yokota, N. Furushiro, S. Komatani, S. Ohzawa, Y. Sato, D. Matsunaga, R. Himeno, T. Higuchi, and A. Makinouchi, "Three-Dimensional Microscopic Elemental Analysis Using an Automated High-Precision Serial Sectioning System", Microscopy and Microanalysis, Vol. 17(2), pp. 246-251, 2011.
- T. Sera, H. Yokota, S. Nakamura, K. Uesugi, M. Hoshino, N. Yagi, T. Ito, K. Hikishima, and H. Okano, "Synchrotron Refraction Enhanced Tomography of an Intact Common Marmoset (Callithrix jacchus)", Open Journal of Radiology, Vol. 1(2), pp. 28-37, 2011.
- F. Liang, K. Fukasaku, S. Takagi, and H. Liu, "A computational model study of the influence of the anatomy of the circle of Willis on cerebral hyperperfusion following carotid artery surgery", Biomedical Engineering Online, Vol. 10, pp. 1-22, 2011.
- R. Kinugasa, Y. Kawakami, T. Fukunaga, and S. Sinha, "Unique Spatial Distribution of In Vivo Human Muscle Activation", Experimental Physiology, Vol. 96(9), pp. 938-948, 2011.
- M. Kanamori, A. Kaiho, Y. Ishizu, Y. Oho, O. Hino, M. Abe, T. Kishimoto, H. Sekihara, Y. Nakamura, H. Suzuki, A. Forrest, and Y. Hayashizaki, "LRRN4 and UPK3B are markers of primary mesothelial cells", PLoS One, Vol. 6(10), pp. e25391-1-e25391-8, 2011.

- 2010:
- S. Yoshizawa, S. Takemoto, M. Takahashi, M. Muroi, S. Kazami, H. Miyoshi, and H. Yokota, "Interactive Registration of Intracellular Volumes with Radial Basis Functions", International Journal of Computational Intelligence and Applications, Vol. 9(3), pp. 207-224, 2010.
- K. Maeshima, H. Iino, S. Hihara, T. Funakoshi, A. Watanabe, M. Nishimura, R. Nakatomi, K. Yahata, F. Imamoto, T. Hashikawa, H. Yokota, and N. Imamoto, "Nuclear pore formation but not nuclear growth is governed by cyclin-dependent kinases (Cdks) during interphase", Nature Structural & Molecular Biology, Vol. 17, pp. 1065–1071, 2010.
- T. Ijiri and H. Yokota, "Contour-based Interface for Refining Volume Segmentation", Computer Graphics Forum: The International Journal of Eurographics Association (Proc. of Pacific Graphics), Vol. 29(7), pp. 2153-2160, 2010.
- J. Nakanishi, Y. Kikuchi, Y. Tsujimura, H. Nakayama, S. Kaneko, T. Shimizu, K. Yamaguchi, H. Yokota, Y. Yoshida, T. Takarada, M. Maeda, and Y. Horiike, "Precise patterning of photoactivatable glass coverslip for fluorescence observation of shape-controlled cells", Supramolecular Chemistry, Vol.22(7), pp. 396-405, 2010.
- S. Yoshizawa, A. Belyaev, and H. Yokota, "Fast Gauss Bilateral Filtering", Computer Graphics Forum: The International Journal of Eurographics Association, Vol.29(1), pp. 60-74, 2010.
- K. Fujisaki, H. Yokota, N. Hiroki, Y. Yamagata, T. Nishikawa, T. Udagawa, and A. Makinouchi, "Observation of three-dimensional internal structure of steel materials by means of serial sectioning with ultrasonic elliptical vibration cutting", Journal of Microscopy, Vol.237(1), pp. 89-95, 2010.
- Y. Endo, J. Sakamoto, Y. Kashiwano, H. Yokota, S. Nakamura, and E. Kinoshita, "A biomechanical study on burst mechanisms of plant fruit: stress analysis of pericarps before bursting", Journal of the Mechanical Behavior of Biomedical Materials, Vol. 3(7), pp. 512-519, 2010.

- 2009:
- M. Takahashi and T. Kobayashi, "Cholesterol regulation of rab-mediated sphingolipid endocytosis", Glycoconjugate Journal Vol. 26(6), pp. 705-710, 2009.
- J. Kimura, N. Kakusho, K. Yamazawa, Y. Hirano, Y. Nambo, H. Yokota, and R. Himeno, "Stereolithographic biomodeling of equine ovary based on 3D serial digitizing device", Journal of Veterinary Science, Vol.10(2), pp. 161-163, 2009.
- T. Ijiri, K. Takayama, H. Yokota, and T. Igarashi, "ProcDef: Local-to-global Deformation for Skeleton-free Character Animation", Computer Graphics Forum: The International Journal of Eurographics Association (Proc. of Pacific Graphics), Vol.28(7), pp. 1821-1828, 2009.
- K. Fujisaki, H. Yokota, N. Furushiro, Y. Yamagata, T. Taniguchi, R. Himeno, A. Makinouchi, and T. Higuchi, "Development of ultra-fine-grain binderless cBN tool for precision cutting of ferrous materials", Journal of Materials Processing Technology, Vol.209(15-16), pp. 5646-5652, 2009.
- S. Takemoto, H. Yokota, T. Mishima, and R. Himeno, "Segmentation of Anatomical Structure by Using a Local Classifier Derived from Neighborhood Information", Advances in Soft Computing: Human-Computer Systems Interaction, Vol.60, pp. 171-180, 2009.
- Y. Hirano, J. Kimura, Y. Nambo, H. Yokota, S. Nakamura, S. Takemoto, R. Himeno, T. Mishima, M. Matsui, and Y.-I. Miyake, "Population of Follicles and Luteal Structures during the Oestrous Cycle of Mares Detected by Three-Dimensional Internal Structure Microscopy", Anatomia, Histologia, Embryologia, Vol. 38(3), pp. 214–218, 2009.

- 2008:
- H. Nishida, T. Suzuki, Y. Tsujimura, S. Komatsu, and Y. Hayashizaki, "An epigenetic aberration increased in intergenic regions of cloned mice", Mammalian Genome, Vol.19, pp. 667-674, 2008.
- T. Sera, H. Yokota, K. Fujisaki, H. Tachibana, K. Uesugi, N. Yagi, and R. Himeno, "Development of high resolution 4D in vivo-CT for visualization of cardiac and respiratory deformations of small animals", Physics in Medicine and Biology, Vol.53(16), pp. 4285-4301, 2008.
- S. Yoshizawa, A. Belyaev, H. Yokota, and H.-P. Seidel, "Fast, Robust, and Faithful Methods for Detecting Crest Lines on Meshes", Computer Aided Geometric Design, Vol.25(8), pp. 545-560, 2008.
- K. Yamazawa, M. Anzai, H. Yokota, R. Himeno, H. Suzuki, H. Narahara, and S. Suzuki, "Trial Formation of Artificial Bone by Inkjet Powder-Layered Manufacturing", International Journal of Automation Technology, Vol.2(3), pp. 156-161, 2008.
- M. Ichikawa, Y. Oho, K. Shimokawa, S. Kondo, S. Nakamura, H. Yokota, R. Himeno, K. Lesch, and Y. Hayashizaki, "Expression analysis for inverted effects of serotonin transporter inactivation", Biochemical and Biophysical Research Communications, Vol.368, pp. 43-49, 2008.
- Y. He, R. Himeno, H. Liu, H. Yokota, and G. Zhi, "Finite element numerical analysis of blood flow and temperature distribution in three-dimensional image-based finger model", International Journal of Numerical Methods for Heat & Fluid Flow, Vol.18(7), pp. 932-953, 2008.
- M. Rajendra, A. Yamamoto, T. Oda, H. Kataoka, H. Yokota, R. Himeno, and T. Higuchi, "Motion generation in MR environment using electrostatic film motor for motion triggered cine-MRI", IEEE/ASME Transactions on Mechatronics, Vol.13(3), pp. 278-285, 2008.

- 2007:
- S. Yoshizawa, A. Belyaev, and H. Seidel, "Skeleton-based variational mesh deformations", Computer Graphics Forum: The International Journal of Eurographics Association (Proc. of EUROGRAPHICS), Vol.26(3), pp. 255-264, 2007.
- M. Takahashi, M. Murate, M. Fukuda, S. Sato, O. Akinori, and T. Kobayashi, "Cholesterol controls lipid endocytosis through rab11", Molecular Biology of the Cell, Vol.18(7), pp. 2667-2677, 2007.

- 2006:
- Y. Hirano, J. Kimura, Y. Nambo, H. Yokota, S. Nakamura, S. Takemoto, R. Himeno, T. Mishima, M. Matsui, and Y. Miyake, "Observation of ovarian internal structures during the estrous cycle of mares", Animal Reproduction Science, Vol.94, pp. 210-214, 2006.

- 2005:
- J. Kimura, Y. Hirano, S. Takemoto, Y. Nambo, T. Ishinazaka, T. Mishima, S. Tsumagari, and H. Yokota, "Three-Dimensional Reconstruction of the Equine Ovary", Anatomia, Histologia, Embryologia, Vol.34, pp. 48-51, 2005.
- K. Sakamaki, C. Takagi, J. Yoshino, H. Yokota, S. Nakamura, K. Kominami, A. Hyodo, K. Takamune, M. Yuge, and N. Ueno, "Transgenic frogs expressing the highly fluorescent protein venus under the control of a strong mammalian promoter suitable for monitoring living cells", Developmental Dynamics, Vol. 233(2), pp. 562–569, 2005.

- 2004:
- S. Takemoto, H. Yokota, Y. Hirano, S. Nakamura, J. Kimura, Y. Nambo, S. Tsumagari, R. Himeno, and T. Mishima, "Semi-automated color segmentation from a biological cross-sectional image series: Follicle segmentation from the equine ovary", IEEE International Conference on Systems, Man and Cybernetics, Hague, Netherlands, Vol. 4, pp. 3076-3081, 2004.
- T. Sera, H. Fujioka, H. Yokota, A. Makinouchi, R. Himeno, R. Schroter, and K. Tanishita, "Localized compliance of small airways in excised rat lungs using microfocal X-ray computed tomography", J. Appl. Physiol., Vol. 96(5), pp. 1665-1673, 2004.

### International Conference Papers (Refereed Paper)

- 2019:
- T. Michikawa, S. Wada, H. Yokota, G. An, M. Akiba, K. Omodaka, and T. Nakazawa, "Retinal Thickness Analysis in High Myopia based on Medial Axis Transforms", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 2805-2808, Berlin, Germany, 2019
- G. An, H. Yokota, N. Motozawa, S. Takagi, M. Mandai, S. Kitahata, Y. Hirami, M. Takahashi, Y. Kurimoto, and M. Akiba, "Deep Learning Classification Models Built with Two-step Transfer Learning for Age Related Macular Degeneration Diagnosis", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 2049-2052, Berlin, Germany, 2019.
- Y.-H. Chang, K. Abe, H. Yokota, K. Sudo, Y. Nakamura, S. Chu, C. Hsu, and M.-D. Tsai, "Human Induced Pluripotent Stem Cell Reprogramming Prediction in Microscopy Images using LSTM based RNN", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 2416-2419, Berlin, Germany, 2019.
- K. Akimoto, S. Tsuichihara, T. Takamatsu, K. Soga, H. Yokota, M. Ito, N. Gotoda, and H. Takemura., "Evaluation of laser-induced plasma ablation focusing on the difference in pulse duration", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 6987-6990, Berlin, Germany, 2019.
- T. Kitrungrotsakul, X.-X Han, Y. Iwamoto, S. Takemoto, H. Yokota, S. Ipponjima, T. Nemoto, X. Wei, and Y.-W. Chen, "A Cascade of CNN and LSTM Network with 3D Anchors for Mitotic Cell Detection in 4D Microscopic Image", IEEE International Conference on Acoustics, Speech and Signal Processing, pp. 1239-1243, Brighton, UK, 2019.

- 2018:
- S. Miyagawa, S. Yoshizawa, and H. Yokota, "Trimmed Median PCA for Robust Plane Fitting", Proc. of IEEE International Conference on Image Processing, pp. 753-757, Athens, Greece, 2018.
- Y. Sakai, S. Takemoto, K. Hori, M. Nishimura, H. Ikematsu, T. Yano, and H. Yokota, "Automatic Detection of Early Gastric Cancer in Endoscopic Images Using a Transferring Convolutional Neural Network", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 4138-4141, Honolulu, USA, 2018.
- Y.-H. Chang, H. Yokota, K. Abe, and M.-D. Tsai, "Three-Dimensional Segmentation of Mouse Embryonic Stem Cell Nuclei for Quantitative Analysis of Differentiation Activity Using Time-Lapse Fluorescence Microscopy Images", Proc. of IEEE International Conference on Bioinformatics and Bioengineering, pp. 299-304, Taichung, 2018.

- 2017:
- D. Bashkirova, S. Yoshizawa, R. Latypov, and H. Yokota, "Fast L1 Gauss 2D Image Transforms", Proc. of Spring/Summer Young Researchers' Colloquium on Software Engineering, pp. 145-149, Innopolis, Russia, 2017.
- Y.-H. Chang, K. Abe, H. Yokota, K. Sudo, Y. Nakamura, C.-Y. Lin, M.-D. Tsai, "Human induced pluripotent stem cell region recognition in microscopy images using Convolutional Neural Networks", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 4058-4061, Jeju, Korea, 2017.
- Y.-H. Chang, K. Abe, H. Yokota, K. Sudo, Y. Nakamura, C.-Y. Lin, M.-D. Tsai, "Human induced pluripotent stem cell region recognition in microscopy images using Convolutional Neural Networks", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 4058-4061, Jeju, Korea, 2017.
- 2016:
- Y.-H. Chang, H. Yokota, K. Abe, J. H. Liu, and M.-D. Tsai, "Detection and Localization of Mouse Induced Pluripotent Stem Cell Formation Using Time-Lapse Fluorescence Microscopy Images", Proc. of International Conference of the IEEE Engineering in Medicine and Biology Society, pp. 3914-3917, Orlando, FL, US, 2016.
- Y.-H. Chang, H. Yokota, K. Abe, C.-C. Li, and M.-D. Tsai, "Fluorescence Microscopy Image Processing and Visualization for Analyzing Cell Kinematics, Proliferation and Attachment in Mouse Embryonic Stem Cell Culture", Proc. of IEEE International Conference on Bioinformatics and Bioengineering, pp. 222-229, Taichung Taiwan, 2016.
- 2014:
- S. Yoshizawa and H. Yokota, "Fast L1 Gaussian Convolution via Domain Splitting", Proc. of IEEE International Conference on Image Processing, pp. 2908-2912, Paris, France, 2014.
- N. Yamashita, S. Yoshizawa and H. Yokota, "Volume-based Shape Analysis for Internal Microstructure of Steels", Proc. of IEEE International Conference on Image Processing, pp. 4887-4891, Paris, France, 2014. Top 10% Paper Award.
- T. Ijiri et al., ACM SIGGRAPH, 2014.
- 2013:
- S. Takemoto, S. Yoshizawa, Y. Tsujimura, and H. Yokota, "A novel performance evaluation system for fluorescent cell image segmentation", Proc. of International Symposium on Computing and Networking, pp. 294-299, (BIR'13: Int. Workshop on BioImage Recognition), Matsuyama, Japan, 2013.
- M. Morita, T. Tawara, M. Nishimura, S. Yoshizawa, B. Chou, I. Kuroki, T. Ijiri, Y. Tsujimura, R. Himeno, and H. Yokota, "Biomedical Image Communication Platform", Proc. of International Symposium on Computing and Networking, pp. 281-287, (BIR'13: Int. Workshop on BioImage Recognition), Matsuyama, Japan, 2013.
- S. Yoshizawa and A. Belyaev, "Möbius-invariant surface energies and ridges", The Mathematics of Surfaces XIV, pp. 109-125, Birmingham, UK, 2013.
- T. Ijiri et al., EUROGRAPHICS, 2013.
- 2012:
- S. Yoshizawa and A. Belyaev, "Conformally Invariant Energies and Minimum Variation Surfaces", Proceedings of Geometric Computing and CAD Workshop, Asian Conference on Design and Digital Engineering, pp. 20:1-20:9, Niseko, Japan, 2012.
- Y. Nagai, Y. Ohtake, H. Yokota, and H. Suzuki, "Boundary Representable Partition of Unity for Image Zooming", Proceedings of Geometric Computing and CAD Workshop, Asian Conference on Design and Digital Engineering, pp. 60:1-60:9, Niseko, Japan, 2012.
- 2010:
- T. Ijiri et al., Pacific Graphics, 2010.
- Y. Nagai, Y. Ohtake, H. Suzuki, and H. Yokota, "Outlier/Noise-robust Partition of Unity Implicit Surface Reconstruction", Proceedings of Geometric Computing Workshop, Asian Conference on Design and Digital Engineerin, pp.454-460, Jeju, Korea, 2010.
- S. Yoshizawa, A. Belyaev, and H. Yokota, "Curvature Extremalities for Intelligent Shape and Image Interrogation", Proceedings of International Conference on Geometry and Graphics, Japan, Kyoto, pp. 242:1-242:10, 2010.
- 2009:
- S. Takemoto, and H. Yokota, "Algorithm Selection for Intracellular Image Segmentation based on Region Similarity", Proceedings of International Conference on Intelligent Systems Design and Applications, IEEE Computer Society, Italy, Pisa, pp. 1413-1418, 2009.
- S. Yoshizawa, S. Takemoto, M. Takahashi, M. Muroi, S. Kazami, H. Miyoshi, and H. Yokota, "Intracellular Volume Registration", Proceedings of International Conference on Intelligent Systems Design and Applications, IEEE Computer Society, Italy, Pisa, pp. 1407-1412, 2009.
- T. Ijiri et al., Pacific Graphics, 2009.

- 2008:
- S. Takemoto, H. Yokota, R. Himeno, and T. Mishima, "Segmentation of Anatomical Structure by Using a Local Classifier Derived from Neighborhood Information", IEEE International Conference on Human System Interaction, Krakow, Poland, pp. 726-730, 2008.
- H. Kataoka, S. Noda, H. Yokota, S. Takagi, R. Himeno, and S. Okazawa, "Simulations of needle insertion using Eulerian hydrocode FEM and experimental validations", Proceedings of International Conference on Medical Image Computing and Computer Assisted Intervention, New York, USA, pp. 560-568, 2008.

- 2007:
- T. Sera, K. Uesugi, N. Yagi, H. Yokota, K. Fujisaki, K. Fukasaku, and R. Himeno, "In vivo-CT system with respiratory and cardiac gating using synchrotron radiation", Proceedings of SPIE-The International Society for Optical Engineering, Vol.6511, pp. 651103-1-651103-9, 2007.
- S. Yoshizawa et al., EUROGRAPHICS, 2007.
- S. Yoshizawa, A. Belyaev, H. Yokota, and H.-P. Seidel, "Fast and faithful geometric algorithm for detecting crest lines on meshes", Proceedings of Pacific Graphics, IEEE Computer Society, USA Maui, pp. 231-237, 2007.

- 2003:
- S. Takemoto, H. Yokota, R. Himeno, A. Makinouchi, and T. Mishima, "Bi-directional segmentation from the color image sequence for in-vivo visualization", Proceedings of International Technical Conference on Circuits/Systems, Computers and Communications, Phoenix park, Korea, pp. 651-654, 2003.

### International Invited Talks, Conferences, Symposiums, and Workshops

- 2019:
- S. Yoshizawa, "Edge-aware Image Filters via Domain Splitting L1 Gaussian Convolutions", Invited Minisymposia Talk, International Congress on Industrial and Applied Mathematics, Valencia University, Valencia, Spain, 2019.
- M. Morita, S. Takemoto, M. Nishimura, Y. Morii, M. Maeda, Y. Okumura, Y. Yamaguchi, and H. Yokota, "A cloud-based communication platform for image-based brain research", poster, International Symposium of Brain/MINDS ISBM2019, Tokyo University, Tokyo, 2019.
- H. Yokota, S. Yoshizawa, S. Takemoto, M. Morita, T. Sera, M. Nishimura, Y. Tsujimura, S. Nakamura, and T. Michikawa, "Bioimage Processing", Resonance Bio International Symposium, Tokyo Univ. of Science, Japan, 2019.
- S. Shimozono, S. Nakamura, H. Yokota, and A. Miyawaki, "RAome - omics of RA", Resonance Bio International Symposium, poster, Tokyo Univ. of Science, Japan, 2019.
- M. Umezawa, T. Sera, H. Yokota, M. Kamimura, and K. Soga, "Computed Tomography for In Vivo Deep Over-Thousand-Nanometer Near-Infrared (OTN-NIR) Fluorescence Imaging", Resonance Bio International Symposium, poster, Tokyo Univ. of Science, Japan, 2019.
- S. Yoshizawa, S. Miyagawa, and H. Yokota, "Trimmed Median PCA", Resonance Bio International Symposium, poster, Tokyo Univ. of Science, Japan, 2019.
- M. Morita, M. Nishimura, S. Takemoto, Y. Tsujimura, and H. Yokota, "Cloud-based image processing system: RBICP", Resonance Bio International Symposium, poster, Tokyo Univ. of Science, Japan, 2019.
- Y.-W. Chen, T. Kitrungrotsakul, X.-H. Han, Y. Iwamoto, J. Liu, S. Takemoto, H. Yokota, S. Ipponjima, and T. Nemoto, "An End-to-end CNN and CLSTM Network with 3D Anchors for Mitotic Cell Detection in 4D Microscopic Images", Resonance Bio International Symposium, poster, Tokyo Univ. of Science, Japan, 2019.
- M. Umebayashi, S. Takemoto, L. Reymond, M. Sundukova, A. Bucci, P.A. Heppenstall, H. Yokota, K. Johnsson, H. Riezman, “Receptor-linked environment-sensitive probe reveals the heterogeneity of local-membrane environment surrounding the insulin receptor”, International Conference on the Bioscience of Lipids, 2019.

- 2018:
- Y. Okamura-Oho, D. Miyamoto, H. Ikeno, M. Morita, H. Yokota, S. Wemler, A. Sato, T. Furuichi, Y. Okumura, and Y. Yamaguchi, "2D/3D image integration on the BAH viewer", poster, Neuroscience 2018, San Diego, CA, 2018.
- M. Morita, "ViBrism DB and the 2D/3D viewer, BAH Viewer", demonstration, Neuroscience 2018, San Diego, CA, 2018.
- S. Yoshizawa, "Fast and accurate edge-aware image filters", Invited Talk, ABiS-GBI-OIST-RB Joint Symposium: Frontiers in Bioimaging, Okinaka, Japan, 2018.
- S. Yoshizawa, S. Nakamura, and H. Yokota, "3D Beef Marbling Extraction", poster, International Meeting on Bioimaging for Young Researchers, Okinaka, Japan, 2018.
- M. Watanabe, Y. Tsujimura, S. Oyama, K. Yamazawa, and H. Yokota, "Development of new binder jetting process for fabricating bone regeneration implants", poster, Society For Biomaterials Annual Meeting, Atlanta, US, 2018.
- S. Oyama, M. Watanabe, Y. Tsujimura, K. Yamazawa, and H. Yokota, "In Vivo Study of Stable Alpha-TCP Scaffolds Fabricated by Modified Binder Jetting", Society For Biomaterials Annual Meeting, Atlanta, US, 2018.
- S. Otsuka, M. Yamamoto, S. Oyama, H. Hirata, H. Mizoguchi, and H. Yokota, "Quantitative Analysis of Arthroscopic Operation in Elbow Arthroscopy", Refereed poster, International Conference of the IEEE Engineering in Medicine and Biology Society, Honolulu, USA, 2018.
- A. Alkandari, F. Costen, J.-P. Berenger, R. Himeno, and H. Yokota, "Comparison of Implementations of Thin Layers in the FDTD Grid", IEEE International Symposium on Antennas and Propagation and USNC-URSI Radio Science Meeting, Boston, US, 2018.
- K. Hori, H. Ikematsu, K. Shinmura, Y. Yoda, Y. Oono, S. Takemoto, H. Yokota, and T. Yano, "The Diagnostic artificial Intelligence (AI) System for Detection of Colon Polyps with High Efficiency of Deep Learning", Digestive Disease Week, Washington, US: Gastrointestinal Endoscopy, Vol. 87(6), Supplement, pp. AB240-AB241, 2018.
- K. Hori, S. Takemoto, Y. Sakai, K. Shinmura, Y. Yoda, Y. Ohno, H. Ikematsu, H. Yokota, T. Yano, “Automatic Detection of Early Gastric Cancer in Endoscopic Images Using a Transferring Convolutional Neural Network”, United European Gastroenterology Week, 2018.

- 2017:
- H. Yokota, "Patient Specific Surgical Simulation achieved by Multi Dimensional Medical Imaging Processing", Intelligent Functional Reconstruction of the Hand, p22, Nagoya, 2017.
- H. Yokota, "Bioimage processing", International Symposium on Imaging Frontier 2017, Tokyo University of Science, Tokyo, 2017.
- S. Takemoto, M. Umebayashi, M. Morita, H. Riezman, and H. Yokota, "Sommelier: A system for performance evaluation of image segmentation methods toward better objectivity of cell image analysis", Taiwan-Japan Joint Meeting on Bioimaging for Young Researchers, poster, Academia Sinica, Taipei, 2017.
- M. Morita, G. Masumoto, M. Nishimura, Y. Tsujimura, S Takemoto, S. Yoshizawa, R. Himeno, and H. Yokota, "Cloud computing system for image processing and sharing in 4D Cell project", Taiwan-Japan Joint Meeting on Bioimaging for Young Researchers, poster, Academia Sinica, Taipei, 2017.
- D. Bashkirova, S. Yoshizawa, and H. Yokota, "Fast Image Filtering with L1 Gauss Transform", International Computer Vision Summer School (ICVSS), poster, Sicily, Italy, 2017.
- S. Takemoto, "Performance evaluation of image segmentation methods for better objectivity of cell image analysis", Invited, NCCR Special Lecture series, Geneva Univ., Geneva, Switzerland, 2017.
- M. Yamamoto, T. Tawara, S. Oyama, Y. Murakami, H. Yokota, and H. Hirata, "Augmented Reality-enhanced Elbow Arthroscopy: N/A - not a clinical study", Annual Meeting of the American Society for Surgery of the Hand: Evolution, Exploration, Empowerment, San Francisco, US: The Journal of Hand Surgery, Vol. 42(9), Supplement, pp. S51-S52, 2017.
- T. Sakamoto, S. Kimura, T. Sera, H. Yokota, K. Ono, and G. Tanaka, "Transitional Flow in the Nasal Cavity", JSME-KSME Thermal and Fluids Engineering Conference, Okinawa, Japan, 2017.
- K. Shimokawa, M. Morita, M. Nishimura, H. Yokota, S. Wemler, Y. Okumura, Y. Yamaguchi, Y. Okamura-Oho, “ViBrism database for gene expression maps and co-expression networks analysis on the 3D brain”, Neuroscience, 2017.
- Y. Nakagawa, A. Saito, J. Hata, S. Takemoto, Y. Komaki, E. Sasaki, H. Okano, H. Yokota, and A. Shimizu, “MRI Image Segmentation of Marmoset Brain Using Prediction of Shape Development by Gaussian Process”, International Forum on Medical Imaging in Asia, 2017.

- 2016:
- T. Sera, H. Kuninaga, K. Fukasaku, H. Yokota, and M. Tanaka, “Influence of Standardization of Airway Geometry on Airflow and Particle Transport”, Summer Biomechanics, Bioengineering, and Biotransport Conference, 2016.
- Y. Okamura-Oho, K. Shimokawa, M. Morita, M. Nishimura, and H. Yokota, "Anatomical and topological expression analysis of the mouse transcriptome in the virtual 3D MRI image spaces of the postnatal brain stages", Neuroinformatics, 2016.

- 2015:
- H. Kuninaga, T. Sera, K. Fukasaku, H. Yokota, and M. Tanaka, “Effect of heterogeneous ventilation on the airway flow and particle deposition in human lung”, Asian Pacific Conference on Biomechanics, 2015.

- 2014:
- G. Tanaka, F. Araki, S. Shimizu, T. Sera, H. Yokota, and K. Ono, "Voxel-Based Simulation of Air-Conditioning in the Human Nasal Cavity", International Heat Transfer Conference, Kyoto, Japan, 2014.
- F. Costen, H. Almeer, J.-P. Berenger, R. Himeno, and H. Yokota, "Huygens Absorbing Boundary Condition", IEEE International Symposium on Antennas and Propagation and USNC-URSI Radio Science Meeting, Memphis, Tennessee, USA, 2014.
- F. Costen, J.-P. Berenger, R. Himeno, and H. Yokota, "Scaling the Huygens Absorbing Boundary Condition code on shared memory architecture", International Conference on Computation in Electromagnetics, Imperial College London, UK, 2014.
- T. Kai, T. Shinohara, K. Oikawa, M. Segawa, H. Iikura, M. Harada, T. Nakatani, M. Ooi, H. Sato, T. Kamiyama, H. Yokota, T. Sera, K. Mochiki, and Y. Kiyanagi, "Progress of Constructing Energy-Resolved Neutron Imaging System at J-PARC MLF", International Workshop on Neutron Wavelength Dependent Imaging, Technische Universitaut Munchen, Garching, Germany, 2014.

- 2013:
- S. Yoshizawa and H. Yokota, "Filtering and Registration of Cell and Intracellular Images", Invited, SEP: School of Engineering & Physical Sciences Seminar, Heriot-Watt University, Edinburgh, UK, 2013
- S. Yoshizawa, "Shape Aesthetics and Features via Möbius Invariants", Invited, Institute of Perception, Action and Behaviour Seminar, Edinburgh University, Edinburgh, UK, 2013.
- S. Yoshizawa and H. Yokota, "Poisson Image Analogy: Texture-Aware Seamless Cloning", EUROGRAPHICS, Refereed poster, Poster Proc. pp. 5-6, Girona, Spain, 2013. Springer Prize for the Best Eurographics Poster 2013.
- K. Fukasaku, M. Negoro, H. Yokota, T. Sera, Y. Yamagata, Y. Ootake, K. Hirota, K. Yamazawa, S. Morita, K. Fukui, Y. Konishi, I. Nara, and S. Shiokawa, "Three dimensional structure of detached coils in aneurysm by neutron beam CT", the 12th Congress of the WFITN, Buenos Aires, Argentina, 2013.
- K. Fukasaku, M. Negoro, H. Yokota, S. Nakamura, T. Ijiri, M. Morita, I. Nara, Y. Konishi, Y. Shiokawa, Y. Konishi, I. Nara, and S. Shiokawa, "Fine structure at the tail of detachable coils", the 12th Congress of the WFITN, Buenos Aires, Argentina, 2013.
- M. Negoro, K. Fukasaku, A. Miyazaki, T. Tanaka, and K. Irie, "Hyperperfusion Sunfrome after Coil Embolization of Cerebral Aneurysms", the 12th Congress of the WFITN, Buenos Aires, Argentina, 2013.
- M. Negoro, F. Arai, T. Fukuda, K. Fukasaku, I. akahashi, and K. Irie, "In vitro Evaluation of Vascular Stress During Aneurysm Embolization", the 12th Congress of the WFITN, Buenos Aires, Argentina, 2013.

- 2012:
- Y. Sato, K. Akita, T. Ijiri, T. Yuichiro, M. Ito, H. Yokota, and N. Saito, "The diversity of pelvic floor by MRI image analysis and histologic reevaluation of its anatomy", The 1st Congress of the Asian Association of Clinical Anatomists, poster, Busan, Korea, 2012.

- 2011:
- S. Yoshizawa, T. Fujiwara, M. Fukuda, and H. Yokota, "Tracking Melanosomes via Particle Filter with Lloyd Partitioning", International Conference on Systems Biology, poster, Mannheim, Germany, 2011.
- T. Ijiri, T. Ashihara, N. Umetani, R. Haraguchi, H. Yokota, T. Igarashi, and K. Nakazawa, "An Efficient, Robust Framework For Simulating the Beating Heart", 23rd Conference of the Society for Medical Innovation and Technology, Tel Aviv, Israel, 2011.
- Y. Sato, T. Ijiri, T. Kobayashi, H. Yokota, and M. Ito, "Semi-automatic Segmentation Tool for Anal Sphincter Muscles", 23rd Conference of the Society for Medical Innovation and Technology, Tel Aviv, Israel, 2011.
- K. Hirota, Y. Yamagata, Y. Otake, S. Morita, J. Ju, S. Wang, H. Yokota, T. Sera, and Y. Iwashita, "Development of imaging detectorfor low neutron flux", 2nd Meeting of The Union for Compact Accelerator-driven Neutron Sources (UCANS-II)", Bloomington, USA, 2011.
- K. Hirota, Y. Yamagata, Y. Otake, S. Morita, J. Ju, S. Wang, H. Yokota, and T. Sera, "Neutron radiography for industrial materials measurement and development of imaging detector for low neutron flux", 1st Asia-Oceania Conference on Neutron Scattering (1st AOCNS), Tsukuba, Japan, 2011.

- 2010:
- S. Takemoto and H. Yokota, "A Supervised Evaluation System of Intracellular Image Segmentation", Invited, Institute of Perception, Action and Behaviour Seminar, Edinburgh University, Edinburgh, UK, 2010.
- S. Yoshizawa, A. Belyaev, and H. Yokota, "Curvature-based Multidimensional Image Creases", Invited, Institute of Perception, Action and Behaviour Seminar, Edinburgh University, Edinburgh, UK, 2010.
- T. Koyama, N. Honda, S. Yoshizawa, Y. Sunaga, S. Noda, S. Ishii, and H. Yokota, "Cell Simulations with Complex 3D Shapes", International Conference on Systems Biology, poster, Edinburgh, UK, 2010.
- S. Takemoto, S. Yoshizawa, and H. Yokota, "A Performance Prediction System for Automatic Intracellular Image Quantization", International Conference on Systems Biology, poster, Edinburgh, UK, 2010.
- Y. Sunaga, S. Yoshizawa, S. Noda, T. Koyama, Y. Tsujimura, and H. Yokota, "A novel simulation platform for cell biochemical reactions, diffusions, and membrane functions", International Conference on Systems Biology, poster, Edinburgh, UK, 2010.
- S. Yoshizawa, A. Belyaev, and H. Yokota, "Feature-Preserving Filters for Biomedical Image Denoising and Clustering", International Conference on Systems Biology, poster, Edinburgh, UK, 2010.
- S. Morita, Y. Yamagata, K. Hirota, S. Mihara, D. T. Dung, H. Sunaga, T. Sera, H. Yokota, T. Shinohara, N. Metoki, and A. Makinouchi, "Neutron radiography for the structural simulation using VCAD system", 19th Meeting of the International Collaboration on Advanced Neutron Sources, poster, Grindelwald, Switzerland, 2010.
- Y. Nagai, Y. Ohtake, and H. Suzuki, "Differential Operators on Arbitrary Dimensional PU Spherical Covers", International Conference on Curves and Surfaces, Avignon, France, 2010.
- T. Sakata, G. Tanaka, T. Sera, N. Kakusho, H. Yokota, K. Ono, and S. Takagi, "Voxel-based modeling of flow in the nasal cavities", Computer Methods in Biomechanics and Biomedical Engineering, Valencia, Spain, 2010.
- S. Oota, A. Yoshiki, H. Yokota, Y. Obata, Y. Nakamura, and R. Himeno, "Of Mice and Men: Biomechanical Modeling as a Tool to Translate Bone Biology Research into Clinical Practice", World Congress on Biomechanics (WCB2010), Singapore Singapore, 2010.
- S. Oota, N. Kakusho, Y. Ikegami, K. Mekada, K. Ayusawa, H. Imagawa, Y. Obata, R. Himeno, H. Yokota, Y. Nakamura, and A. Yoshiki, "Homology Mapping: Development of the Mouse Hindlimb Musculoskeletal Model Using the Human Musculoskeletal Model and Scleraxis(SCX)-GFP Mouse", 24th International Mammalian Genome Conference (IMGC2010), Crete, Greece, 2010.
- S. Morita, Y. Yamagata, K. Hirota, S. Mihara, T. Dinh, H. Sunaga, T. Sera, H. Yokota, T. Shinohara, N. Metoki, and A. Makinouchi, "Thermal neutron radiography and structural simulation using VCAD system software", 1st Meeting of The Union for Compact Accelerator-driven Neutron Sources (UCANS-I), Beijing, China, 2010.

- 2009:
- S. Takemoto and H. Yokota, "Parallelized Performance Evaluation of Image Segmentation Algorithm by using the Linux Cluster on RICC", Supercomputing, poster, Oregon, USA, 2009.
- H. Yokota, K. Fujisaki, N. Furushiro, Y. Yamagata, and N. Yamashita, "Three-dimensional internal structure observation for industrial materials by means of high precision serial sectioning system", Invited, Eighteenth International Conference on Processing and Fabrication of Advanced Materials, Sendai, Japan, 2009.
- S. Yoshizawa, A. Belyaev, and H. Yokota, "Fast Bilateral Image and Volume Processing", Invited, ERPem: Signal and Image Processing Joint Seminar, Heriot-Watt University, Edinburgh, UK, 2009.
- S. Yoshizawa, A. Belyaev, H. Yokota, and H. Seidel, "On surface ridges and their use for shape analysis", Invited, Institute of Perception, Action and Behaviour Seminar, Edinburgh University, Edinburgh, UK, 2009.
- S. Yoshizawa, A. Belyaev, and H. Yokota, "A Novel Approach for Fast and Accurate Bilateral Filtering", Invited, CG Lunch Talk, Max-Planck-Institut fuer Informatik, Saarbruecken, Germany, 2009.
- A. Waggoner, T. Oda, R. Kinugasa, K. Ueno, K. Cheng, H. Yokota, and R. Himeno, "DTI based muscle fiber tractography in humans at 4 Tesla using stimulated-echos", ISMRM 17th Annual Meeting and Exhibition, Honolulu, USA, 2009.

- 2008:
- S. Yoshizawa and H. Yokota, "Image & Geometry Processing for Cell Biology", Invited, ERPem: Signal and Image Processing Joint Seminar, Heriot-Watt University, Edinburgh, UK, 2008.
- S. Yoshizawa, and H. Yokota, "Volume Processing for Cell Biology", Invited, Interactive Media Technology Group Seminar, Durham University, Durham, UK, 2008.
- S. Yoshizawa, A. Belyaev, and H.-P. Seidel, "Natural-Looking Variational Mesh Deformations", Invited, Journal Club: Vision, Image & Signal Processing Group Seminar, Heriot-Watt University, Edinburgh, UK, 2008.

- 2007:
- M. Takahashi, M. Murate, M. Fukuda, S. Sato, O. Akinori, T. Kobayashi, "Cholesterol controls lipid endocytosis through rab11", International Symposium on Membrane Traffic, Awaji, Japan 2007.
- H. Yokota, N. Kakusho, K. Mekada, A. Murakami, S. Nakamura, M. Ito, K. Kase, S. Oota, K. Fukami, H. Masuya, S. Wakana, K. Moriwaki, T. Shiroishi, R. Himeno, Y. Obata, and A. Yoshiki, "High-Resolution full color digital mouse anatomy by three-dimensional internal structure microscopy", 21st International Mammalian Genome Conference, Kyoto, Japan, 2007.
- K. Fujisaki, H. Yokota, N. Furushiro, S. Komatani, S. Ohzawa, Y. Sato, R. Himeno, T. Higuchi, and A. Makinouchi, "Three-dimensional Microscopic Elemental Analyses based on X-ray Fluorescence Analysis combined with NC High-precision Machining Process", 19th International Congress on X-Ray Optics and Microanalysis, Kyoto, Japan, 2007.

- 2006:
- H. Yokota, M. Nishimura, K. Fukasaku, S. Noda, H. Shimai, S. Nakamura, R. Himeno, and A. Makinouchi, "Construction of Integrated Mechanical Simulation Model of Whole Body for Alive Human", World Congress on Medical Physics and Biomedical Engineering, Seoul Korea, 2006.
- D. Kobayashi, H. Yokota, S. Morishita, S. Nakamura, R. Himeno, T. Mishima, and K. Fukasaku, "Quantitative Representation of Cerebral Aneurysm by Tree Graph", 31st Congress & 15th Advanced Course and 3rd International Intracranial Stent Meeting, Geneva, Switzerland, 2006.

- 2005:
- M. Takeuchi, H. Yokota, F. Raible, M. Brand, H. Okamoto, and I. Masai, "Vax transcription factory control cell movement of optic stalk and formation of optic cup", 4th European Zebrafish Genetics and Development Meeting, Dresden, Germany, 2005.

- 2004:
- H. Yokota, S. Nakamura, N. Kakusho, R. Kawaguchi, H. Yabe, A. Makinouchi, R. Himeno, and T. Higuchi, "New anatomy with three dimension internal structure microscope device", 16th International Congress of the IFAA: Anatomical Science from Gene to Body, Kyoto, Japan, 2004.
- J. Kimura, Y. Hirano, S. Takemoto, Y. Nanbo, G. Ishinazaka, R. Himeno, T. Mishima, S. Tumagari, and H. Yokota, "Three-dimensional reconstruction of the equine ovary", 16th International Congress of the IFAA: Anatomical Science from Gene to Body, Kyoto, Japan, 2004.

Remarks: the following list includes the part of international publications and presentations, where their authors or presenters are/were the members of "Image Processing Research Team", "Bio-research Infrastructure Construction Team", or "VCAT Development Team". Here the domestic publications and presentations are excluded. See also the author's/presenter's own pages for their complete lists of publications and presentations.