Computerized model building of brain neuronal network

• Project/Area Number: 25610126
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Biological physics/Chemical physics/Soft matter physics
• Research Institution: Tokai University
• Principal Investigator: Mizutani Ryuta 東海大学, 工学部, 教授 (70272482)
• Co-Investigator(Renkei-kenkyūsha): TAKEKOSHI Susumu 東海大学, 医学部, 教授 (70216878)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000); Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2014: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2013: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: 神経回路 / マイクロCT / マイクロトモグラフィ

Outline of Final Research Achievements

Brain is composed of a huge number of neurons, which constitute neuronal circuits. The first step to analyzing such brain circuits is to trace neuronal networks to build three-dimensional models of their complicated structures. In this study, we have developed methods for building three-dimensional wire models by tracing neuronal networks. We evaluated a number of algorithms reported for tracing wire-form structures in two-dimensional images. Some of those methods were proven to be effective in the computerized building of neuronal network model. A part of this study has been published as a feature article of the September 2015 issue of Microscopy Today, the official publication of the Microscopy Society of America.

Research Products

• [Journal Article] A method for estimating spatial resolution of real image in the Fourier domain. (2016)
  • Author(s): Mizutani R, Saiga R, Takekoshi S, Inomoto C, Nakamura N, Itokawa M et al.
  • Journal Title: J Microsc. Volume: 261 Issue: 1 Pages: 57-66
  • DOI: 10.1111/jmi.12315
  • Peer Reviewed
• [Journal Article] Recent progress of hard x-ray imaging microscopy and microtomography at BL37XU of SPring-8 (2016)
  • Author(s): Yoshio Suzuki, Akihisa Takeuchi, Yasuko Terada, Kentaro Uesugi, and Ryuta Mizutani
  • Journal Title: AIP Conf. Proc. Volume: 1696 Pages: 020013-020013
  • DOI: 10.1063/1.4937507
  • Peer Reviewed / Open Access
• [Journal Article] Three-dimensional structure of brain tissue at submicrometer resolution. (2016)
  • Author(s): Rino Saiga, Ryuta Mizutani, Chie Inomoto, Susumu Takekoshi, Naoya Nakamura, Akio Tsuboi, Motoki Osawa, Makoto Arai, Kenichi Oshima, Masanari Itokawa, Kentaro Uesugi, Akihisa Takeuchi, Yasuko Terada, and Yoshio Suzuki
  • Journal Title: AIP Conf. Proc. Volume: 1696 Pages: 020004-020004
  • DOI: 10.1063/1.4937498
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Three-Dimensional Neuronal Structure of Human Cerebral Cortex Determined by Synchrotron-Radiation Microtomography. (2015)
  • Author(s): Saiga R, Takekoshi S, Inomoto C, Nakamura N, Tsuboi A, Osawa M, Arai M, Oshima K, Itokawa M, Uesugi K, Takeuchi A, Terada Y, Suzuki Y and Mizutani R.
  • Journal Title: Microsc. Microanal Volume: 21 Issue: S3 Pages: 919-920
  • DOI: 10.1017/s1431927615005395
  • Peer Reviewed / Open Access
• [Journal Article] X-ray tomographic microscopy of Drosophila brain network and skeletonized model building in the three-dimensional image (2015)
  • Author(s): Ryuta Mizutani, Rino Saiga, Kentaro Uesugi, Akihisa Takeuchi, Yasuko Terada, and Yoshio Suzuki
  • Journal Title: Microsc. Microanal. Volume: 21(S3) Issue: S3 Pages: 917-918
  • DOI: 10.1017/s1431927615005383
  • Peer Reviewed / Open Access
• [Journal Article] Scanning Brain Networks with Micro-CT (2015)
  • Author(s): Ryuta Mizutani, Rino Saiga, Susumu Takekoshi, Makoto Arai, Akihisa Takeuchi, and Yoshio Suzuki
  • Journal Title: Microscopy Today Volume: 23 Issue: 5 Pages: 12-17
  • DOI: 10.1017/s1551929515000784
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT) (2015)
  • Author(s): Masato Ohtsuka, Hiromi Miura, Keiji Mochida, Michiko Hirose, Ayumi Hasegawa, Atsuo Ogura, Ryuta Mizutani, Minoru Kimura, Ayako Isotani, Masahito Ikawa, Masahiro Sato and Channabasavaiah B Gurumurthy
  • Journal Title: BMC Genomics Volume: 16 Pages: 274-274
  • NAID: 120006957412
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT) (2015)
  • Author(s): Ohtsuka M., Miura H., Mochida K., Hirose M., Hasegawa A., Ogura A., Mizutani R., Kimura M., Isotani A., Ikawa M., Sato M. and Gurumurthy C. B.
  • Journal Title: BMC Genomics Volume: in press
  • NAID: 120006957412
  • Peer Reviewed / Open Access
• [Journal Article] SPring-8放射光による神経回路ネットワークの解析 (2014)
  • Author(s): 水谷隆太，雑賀里乃，竹内晃久，上杉健太朗，寺田靖子，鈴木芳生
  • Journal Title: 顕微鏡 Volume: 49(3) Pages: 222-225
  • NAID: 130007701737
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Structural biology of DNA (6-4) photoproducts formed by ultraviolet radiation and interactions with their binding proteins (2014)
  • Author(s): Yokoyama, H. Mizutani, R.
  • Journal Title: Int. J. Mol. Sci. Volume: 15 Issue: 11 Pages: 20321-20338
  • DOI: 10.3390/ijms151120321
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Three-dimensional analysis of neuronal circuits of the human brain by X-ray microtomography (2014)
  • Author(s): Ryuta Mizutani, Rino Saiga, Akihisa Takeuchi, Kentaro Uesugi and Yoshio Suzuki
  • Journal Title: SPring-8 Information Volume: 19 Pages: 225-229
  • Open Access / Acknowledgement Compliant
• [Journal Article] Spatiotemporal development of soaked protein crystal (2014)
  • Author(s): Ryuta Mizutani, Yusuke Shimizu, Rino Saiga, Go Ueno, Yuki Nakamura, Akihisa Takeuchi, Kentaro Uesugi, and Yoshio Suzuki
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 5731-5731
  • DOI: 10.1038/srep05731
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Structure of a double-stranded DNA (6–4) photoproduct in complex with the 64M-5 antibody Fab. (2013)
  • Author(s): Hideshi Yokoyama, Ryuta Mizutani, Yoshinori Satow
  • Journal Title: Acta Crystallographica D Volume: 69 Issue: 4 Pages: 504-512
  • DOI: 10.1107/s0907444912050007
  • Peer Reviewed
• [Journal Article] X-ray microtomographic visualization of Escherichia coli by metalloprotein overexpression (2013)
  • Author(s): Ryuta Mizutani, Keisuke Taguchi, Masato Ohtsuka, Minoru Kimura, Akihisa Takeuchi, Kentaro Uesugi, and Yoshio Suzuki
  • Journal Title: J. Synchrotron Radiation Volume: 20 Issue: 4 Pages: 581-586
  • DOI: 10.1107/s0909049513008467
  • Peer Reviewed
• [Journal Article] Ｘ線マイクロトモグラフィ法によるヒト大脳神経回路の決定 (2013)
  • Author(s): 水谷隆太，雑賀里乃
  • Journal Title: 放射光 Volume: 26 Pages: 268-275
  • NAID: 10031191828
  • Peer Reviewed
• [Journal Article] Three-dimensional network of Drosophila brain hemisphere (2013)
  • Author(s): Ryuta Mizutani, Rino Saiga, Akihisa Takeuchi, Kentaro Uesugi and Yoshio Suzuki
  • Journal Title: J. Struct. Biol. Volume: 184 Issue: 2 Pages: 271-279
  • DOI: 10.1016/j.jsb.2013.08.012
  • Peer Reviewed
• [Presentation] ヒト大脳皮質の神経回路の三次元解析 (2015)
  • Author(s): 藤巻知央，菊池亜弥，蓮見真子，竹腰進，井野元智恵，中村直哉，坪井秋男，大澤資樹，新井誠，大島健一，糸川昌成，上杉健太朗，竹内晃久，寺田靖子，鈴木芳生，雑賀里乃，水谷隆太
  • Organizer: 第88回日本生化学会大会
  • Place of Presentation: 神戸国際会議場（神戸市）
  • Year and Date: 2015-12-01
• [Presentation] X-ray Tomographic Microscopy of Drosophila Brain Network and Skeletonized Model Building in the Three-Dimensional Image (2015)
  • Author(s): Ryuta Mizutani, Rino Saiga, Kentaro Uesugi, Akihisa Takeuchi, Yasuko Terada and Yoshio Suzuki
  • Organizer: Microscopy & Microanalysis 2015 Meeting
  • Place of Presentation: Oregon Convention Center (Portland, USA)
  • Year and Date: 2015-08-04
  • Int'l Joint Research
• [Presentation] Three-Dimensional Neuronal Structure of Human Cerebral Cortex Determined by Synchrotron-Radiation Microtomography (2015)
  • Author(s): Rino Saiga, Susumu Takekoshi, Chie Inomoto, Naoya Nakamura, Akio Tsuboi, Motoki Osawa, Makoto Arai, Kenichi Oshima, Masanari Itokawa, Kentaro Uesugi, Akihisa Takeuchi, Yasuko Terada, Yoshio Suzuki and Ryuta Mizutani
  • Organizer: Microscopy & Microanalysis 2015 Meeting
  • Place of Presentation: Oregon Convention Center (Portland, USA)
  • Year and Date: 2015-08-04
  • Int'l Joint Research
• [Presentation] X-ray microtomographic visualization of microorganisms by metalloprotein overexpression (2014)
  • Author(s): Ryuta Mizutani, Akihisa Takeuchi, Kentaro Uesugi, Yoshio Suzuki.
  • Organizer: The 12th International Conference on X-Ray Microscopy 2014
  • Place of Presentation: Melbourne Convention and Exhibition Centre (Melbourne, Australia)
  • Year and Date: 2014-10-26 – 2014-10-31
• [Presentation] Three-dimensional structure of the fruit-fly brain network (2014)
  • Author(s): Rino Saiga, Ryuta Mizutani, Akihisa Takeuchi, Kentaro Uesugi, Yoshio Suzuki
  • Organizer: The 12th International Conference on X-Ray Microscopy 2014
  • Place of Presentation: Melbourne Convention and Exhibition Centre (Melbourne, Australia)
  • Year and Date: 2014-10-26 – 2014-10-31
• [Presentation] Recent progress of imaging microscopy and microtomography at BL37XU of SPring-8 (2014)
  • Author(s): Yoshio Suzuki, Akihisa Takeuchi, Yasuko Terada, Kentaro Uesugi, and Ryuta Mizutani
  • Organizer: The 12th International Conference on X-Ray Microscopy 2014
  • Place of Presentation: Melbourne Convention and Exhibition Centre (Melbourne, Australia)
  • Year and Date: 2014-10-26 – 2014-10-31
• [Presentation] Building human brain network in electron density map determined by X-ray microtomography (2014)
  • Author(s): Rino Saiga, Susumu Takekoshi, Naoya Nakamura, Akihisa Takeuchi, Kentaro Uesugi, Yoshio Suzuki, and Ryuta Mizutani
  • Organizer: 23rd Congress and General Assembly of the International Union of Crystallography
  • Place of Presentation: Palais des congres de Montreal (Montreal, Canada)
  • Year and Date: 2014-08-05 – 2014-08-12
• [Presentation] Visualizing soaking process of protein crystal (2014)
  • Author(s): Ryuta Mizutani, Yusuke Shimizu, Rino Saiga, Go Ueno, Yuki Nakamura, Akihisa Takeuchi, Kentaro Uesugi, and Yoshio Suzuki
  • Organizer: 23rd Congress and General Assembly of the International Union of Crystallography
  • Place of Presentation: Palais des congres de Montreal (Montreal, Canada)
  • Year and Date: 2014-08-05 – 2014-08-12
• [Presentation] 広視野高分解能硬Ｘ線結像顕微鏡によるマイクロCT (2014)
  • Author(s): 鈴木芳生、寺田靖子、竹内晃久、上杉健太朗、田村繁治、水谷隆太
  • Organizer: 第27回日本放射光学会年会
  • Place of Presentation: 広島国際会議場
• [Presentation] X 線マイクロトモグラフィ法によるヒト大脳神経回路の解析 (2014)
  • Author(s): 水谷隆太
  • Organizer: SPRUC拡大研究会・SPring-8利用ワークショップ
  • Place of Presentation: 高輝度光科学研究センター
  • Invited
• [Presentation] Ｘ線マイクロトモグラフィ法によるヒト脳組織の三次元構造解析 (2013)
  • Author(s): 雑賀里乃、水谷隆太、竹腰進、井野元智恵、中村直哉、大澤資樹、新井誠、大島健一、糸川昌成、竹内晃久、上杉健太朗、鈴木芳生
  • Organizer: 第74回応用物理学会秋季学術講演会
  • Place of Presentation: 同志社大学京田辺校
• [Presentation] Ｘ線マイクロトモグラフィ法によるヒト大脳皮質の三次元構造解析 (2013)
  • Author(s): 水谷隆太、雑賀里乃、竹腰進、井野元智恵、中村直哉、大澤資樹、新井誠、大島健一、糸川昌成、竹内晃久、上杉健太朗、鈴木芳生
  • Organizer: SPring-8 シンポジウム2013
  • Place of Presentation: 京都大学宇治おうばくプラザ
• [Remarks] Mizutani Lab, Tokai Univ
  • URL: http://www.el.u-tokai.ac.jp/ryuta/
• [Remarks] Mizutani Laboratory, Dept of Applied Biochemistry
  • URL: http://www.el.u-tokai.ac.jp/ryuta/
• [Remarks] SPATIOTEMPORAL DEVELOPMENT; NATIVE
  • URL: http://www.rcsb.org/pdb/explore.do?structureId=3WPJ
• [Remarks] SPATIOTEMPORAL DEVELOPMENT; 750 SEC
  • URL: http://www.rcsb.org/pdb/explore.do?structureId=3wpk
• [Remarks] Mizutani Laboratory
  • URL: http://www.el.u-tokai.ac.jp/ryuta/