Creating Gene Expression Based Digital Brain Atlas with Our New Mapping Technique and Map Analysis

• Project/Area Number: 25560428
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Basic / Social brain science
• Research Institution: The Institute of Physical and Chemical Research
• Principal Investigator: OHO Yuko 独立行政法人理化学研究所, 光量子工学研究領域, 客員研究員 (60381571)
• Co-Investigator(Kenkyū-buntansha): YOKOTA Hideo 独立行政法人理化学研究所, 光量子工学研究領域, チームリーダー (00261206)
• Project Period (FY): 2013-04-01 – 2015-03-31
• Project Status: Completed (Fiscal Year 2014)
• Budget Amount: ¥4,030,000 (Direct Cost: ¥3,100,000、Indirect Cost: ¥930,000); Fiscal Year 2014: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2013: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000)
• Keywords: 遺伝子発現 / ３次元脳地図 / バイオインフォマティクス / データベース / 画像処理 / ネットワーク解析 / 共発現解析 / 脳地図

Outline of Final Research Achievements

We fine-tuned our 3D gene expression mapping technique, Transcriptome Tomography, to create data sets of the mouse brain in developmental stages (3d, 7d 3w and 8w after birth) for overviewing comprehensive gene expression in the whole brain 3D anatomical context. We analyzed the data with atlas informatics, which is a new framework to integrate bioinformatics, such as co-expression analysis, and image processing of MRI or block-face images, and then, we have renewed the database, ViBrism DB, as a neuroscience open resource.

Research Products

• [Journal Article] Anatomical landmarks for registration of experimental image data to volumetric rodent brain atlasing templates (2015)
  • Author(s): Sergejeva, M, Papp, E. A., Bakker, R., Gaudnek, M. A., Okamura-Oho, Y., Boline, J., Bjaalie, J. G., Hess, A.
  • Journal Title: J. Neurosci. Methods Volume: 240 Pages: 161-169
  • DOI: 10.1016/j.jneumeth.2014.11.005
  • Peer Reviewed
• [Journal Article] Numerical simulation of airflow and microparticle deposition in a synchrotron micro-CT-based pulmonary acinus model (2015)
  • Author(s): T. Sera, K. Uesugi, N. Yagi, and H. Yokota
  • Journal Title: Computer Methods in Biomechanics and Biomedical Engineering Volume: 18 Issue: 13 Pages: 1427-1435
  • DOI: 10.1080/10255842.2014.915030
  • Peer Reviewed
• [Journal Article] Broad Integration of Expression Maps and Co-Expression Networks Compassing Novel Gene Functions in the Brain (2014)
  • Author(s): Okamura-Oho Y, Shimokawa K, Nishimura M, Takemoto S, Sato A, Furuichi T, Yokota H.
  • Journal Title: Scientific Report Volume: 4 Issue: 1 Pages: 6969-6969
  • DOI: 10.1038/srep06969
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Solvable model for chemical oscillations (2014)
  • Author(s): E. Chikayama, Y. Sunaga, S. Noda, H. Yokota
  • Journal Title: Journal of Mathematical Chemistry Volume: 52 Issue: 2 Pages: 399-406
  • DOI: 10.1007/s10910-013-0275-z
  • Peer Reviewed
• [Journal Article] Whole-brain imaging with single-cell resolution using chemical cocktails and computational analysis. (2014)
  • Author(s): Etsuo A. Susaki, Kazuki Tainaka, Dimitri Perrin, Fumiaki Kishino, Takehiro Tawara, Tomonobu M. Watanabe, Chihiro Yokoyama, Hirotaka Onoe, Megumi Eguchi, Shun Yamaguchi, Takaya Abe, Hiroshi Kiyonari, Yoshihiro Shimizu, Atsushi Miyawaki, Hideo Yokota, Hiroki R. Ueda
  • Journal Title: Cell Volume: 157 Issue: 3 Pages: 726-739
  • DOI: 10.1016/j.cell.2014.03.042
  • Peer Reviewed
• [Journal Article] Prediction of open urinary tract in laparoscopic partial nephrectomy by virtual resection plane visualization (2014)
  • Author(s): D. Ueno, K. Makiyama, H. Yamanaka, T. Ijiri, H. Yokota, and Y. Kubota
  • Journal Title: BMC Urology Volume: 14 Issue: 1 Pages: 47-47
  • DOI: 10.1186/1471-2490-14-47
  • Peer Reviewed / Open Access
• [Journal Article] Communication Platform for Image Analysis and Sharing in Biology (2014)
  • Author(s): M. Morita, T. Tawara, M. Nishimura, S. Yoshizawa, B. Chou, I. Kuroki, T. Ijiri, Y. Tsujimura, R. Himeno, and H. Yokota
  • Journal Title: International Journal of Networking and Computing Volume: 4 Issue: 2 Pages: 369-391
  • DOI: 10.15803/ijnc.4.2_369
  • NAID: 130004709094
  • ISSN: 2185-2839, 2185-2847
  • Peer Reviewed / Open Access
• [Journal Article] Flower Modeling via X-ray Computed Tomography (2014)
  • Author(s): T. Ijiri, S. Yoshizawa, H. Yokota, and T. Igarashi
  • Journal Title: ACM Transactions on Graphics Volume: 33 Issue: 4 Pages: 1-10
  • DOI: 10.1145/2601097.2601124
  • Peer Reviewed
• [Journal Article] Efficient parallel LOD-FDTD method for Debye-dispersive media (2014)
  • Author(s): Tadashi Hemmi, Fumie Costen, Salvador Garcia, Ryutaro Himeno, Hideo Yokota, Mehshan Mustafa
  • Journal Title: IEEE Transactions on Antennas and Propagation Volume: 62 Issue: 3 Pages: 1330-1338
  • DOI: 10.1109/tap.2013.2294860
  • Peer Reviewed
• [Journal Article] オーダーメ─ド再生医療に向けたコンピュータサイエンス (2014)
  • Author(s): 横田秀夫
  • Journal Title: 四国医学雑誌 Volume: 70 Pages: 13-18
• [Journal Article] 16 landmarks of the mouse brain have been validated as fiducials for registration to WHS (2014)
  • Author(s): Marina Sergejeva, Rembrandt Bakker, Andre Gaudnek, Yuko Okamura-Oho, Jyl Boline and Andreas Hess
  • Journal Title: Front. Neuroinform. Volume: -
  • DOI: 10.3389/conf.fninf.2014.08.00028
  • Peer Reviewed
• [Journal Article] Developmentally Conserved Brain Designs Quantifiable with Transcriptome Tomography (2013)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Satoko Takemoto and Hideo Yokota
  • Journal Title: Front. Neuroinform. Volume: -
  • DOI: 10.3389/conf.fninf.2014.08.00130
  • Peer Reviewed
• [Journal Article] Bilateral Hermite Radial Basis Functions for Contour-based Volume Seg- mentation (2013)
  • Author(s): T. Ijiri, S. Yoshizawa, Y. Sato, M. Ito, and H. Yokota
  • Journal Title: Computer Graphics Forum (Proc. of EUROGRAPHICS'13) Volume: 32(2) Issue: 2pt1 Pages: 123-132
  • DOI: 10.1111/cgf.12032
  • Peer Reviewed
• [Journal Article] Boundary Representable Partition of Unity for Image Zooming, (2013)
  • Author(s): Yukie Nagai, Yutaka Ohtake, Hiromasa Suzuki
  • Journal Title: SCIENCE CHINA Information Sciences Volume: 56 Issue: 11 Pages: 1-12
  • DOI: 10.1007/s11432-013-5020-5
  • Peer Reviewed
• [Journal Article] A novel performance evaluation system for fluorescent cell image segmentation (2013)
  • Author(s): Satoko Takemoto, Shin Yoshizawa, Yuki Tsujimura, and Hideo Yokota
  • Journal Title: Proc. of International Symposium on Computing and Networking Volume: - Pages: 294-299
  • DOI: 10.1109/candar.2013.51
  • Peer Reviewed
• [Journal Article] Biomedical Image Communication Platform (2013)
  • Author(s): Masahiko Morita, Takehiro Tawara, Masaomi Nishimura, Shin Yoshizawa, Bukai Chou, Ippei Kuroki, Takashi Ijiri, Yuki Tsujimura, Ryutaro Himeno and Hideo Yokota
  • Journal Title: Proc. of International Symposium on Computing and Networking Volume: - Pages: 281-287
  • DOI: 10.1109/candar.2013.49
  • Peer Reviewed
• [Presentation] Ex-vivo transcriptomic analysis on the web: a new platform of ViBrism DB for gene expression mapping and analysis (2015)
  • Author(s): Yuko Okamura-Oho, Masahiko Morita, Kazuro Shimokawa, Masaomi Nishimura, Takahiro Tawara , Hideo Yokota
  • Organizer: Neuroinformatics 2015
  • Place of Presentation: Cairns, Australia
  • Year and Date: 2015-08-20 – 2015-08-22
• [Presentation] 3次元内部構造顕微鏡による3次元計測の生物・材料分野への挑戦と展開 (2015)
  • Author(s): 於保祐子
  • Organizer: RIKENシンポジウム
  • Place of Presentation: 理化学研究所 仁科センター 大会議室、和光市、埼玉
  • Year and Date: 2015-02-06
  • Invited
• [Presentation] Transcriptome tomography: mapping genes onto 3D brain structures (2014)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Sakiko Nakamura, Yuki Tsujimura, Masaomi Nishimura, Satoko Takemoto, Masahiko Morita, Takashi Ijiri, Takehiro Tawara, Hideo Yokota
  • Organizer: Annual meeting of Society of Neuroscience 2014
  • Place of Presentation: Washington DC, USA
  • Year and Date: 2014-11-15 – 2014-11-19
• [Presentation] Integrated Analysis of Expression Maps and Co-Expression Networks Using a Dataset of ViBrism DB (2014)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Masaomi Nishimura, Satoko Takemoto, Masahiko Morita, Hideo Yokota
  • Organizer: ＡＩＮＩ２０１４
  • Place of Presentation: Wako, Japan
  • Year and Date: 2014-09-25 – 2014-09-26
• [Presentation] Novel genes located in the co-expression networks detected with Transcriptome Tomography (2014)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Masaomi Nishimura, Satoko Takemoto, Akira Sato, Teiichi Furuichi, Hideo Yokota
  • Organizer: Neuroinformatics 2014
  • Place of Presentation: Leiden, Nederland
  • Year and Date: 2014-08-25 – 2014-08-27
• [Presentation] ﾄﾗﾝｽｸﾘﾌﾟﾄｰﾑ･ﾄﾓｸﾞﾗﾌｨｰを用いた遺伝子発現に基づく全脳地図作成 (2014)
  • Author(s): 於保祐子
  • Organizer: 科学技術振興機構主催理化学研究所新技術説明会
  • Place of Presentation: JST 東京本部別館ホール、市ヶ谷、東京
  • Year and Date: 2014-06-12 – 2014-06-13
  • Invited
• [Presentation] Developmentally Conserved Brain Designs Quantifiable with Transcriptome Tomography (2013)
  • Author(s): Yuko Okamura-Oho, Kazuro Shimokawa, Satoko Takemoto and Hideo Yokota
  • Organizer: 5th INCF Congress of Neuroinformatics
  • Place of Presentation: Stockholm, Sweden
• [Presentation] Registration workflows for the creation of INCF digital atlas hubs (2013)
  • Author(s): Jyl Boline, Brian Avants, Richard Baldock, Rembrandt Bakker, Albert Burger, James Gee, Christian Haselgrove, Andreas Hess, Luis Ibanez, Stephen Larson, Piotr Majka, Yuko Okamura-Oho, Seth Ruffins and Ilya Zaslavsky
  • Organizer: 5th INCF Congress of Neuroinformatics
  • Place of Presentation: Stockholm, Sweden
• [Presentation] 16 landmarks of the mouse brain have been validated as fiducials for registration to WHS (2013)
  • Author(s): Marina Sergejeva, Rembrandt Bakker, André Gaudnek, Yuko Okamura-Oho, Jyl Boline and Andreas Hess
  • Organizer: 5th INCF Congress of Neuroinformatics
  • Place of Presentation: Stockholm, Sweden
• [Presentation] Looking back and to the future of the INCF Digital Atlasing Program (2013)
  • Author(s): Jyl Boline, Mike Hawrylycz, Ilya Zaslavsky, INCF Digital Atlasing Standards, Waxholm Space, and Digital Atlasing Infrastructure Task Forces
  • Organizer: Neuroscience 2013
  • Place of Presentation: San Diego, CA USA
• [Presentation] Bilateral Hermite Radial Basis Functions for Contour-based Volume Segmentation (2013)
  • Author(s): T. Ijiri, S. Yoshizawa, Y. Sato, M. Ito and H. Yokota
  • Organizer: Eurographics Association
  • Place of Presentation: Gerona, Spain
• [Presentation] ViBrism-DBデータセットを用いた遺伝子発現地図と共発現ネットワークの統合解析で明らかになった発生学的に保存された脳の意匠
  • Author(s): 於保祐子，下川和郎，竹本智子，横田秀夫
  • Organizer: 日本分子生物学会
  • Place of Presentation: 神戸市
• [Presentation] A novel performance evaluation system for fluorescent cell image segmentation
  • Author(s): S. Takemoto, S. Yoshizawa, Y. Tsujimura, and H. Yokota
  • Organizer: BIR'13: Int. Workshop on BioImage Recognition
  • Place of Presentation: Matsuyama, japan
• [Presentation] Biomedical Image Communication Platform
  • Author(s): M. Morita, T. Tawara, M. Nishimura, S. Yoshizawa, B. Chou, I. Kuroki, T. Ijiri, Y. Tsujimura, R. Himeno, and H. Yokota
  • Organizer: BIR'13: Int. Workshop on BioImage Recognition
  • Place of Presentation: Matsuyama, japan
• [Book] バイオ画像解析手取り足取りガイド, 第３章、５） (2014)
  • Author(s): 森田正彦,西村将臣,横田秀夫
  • Publisher: ,羊土社
• [Remarks] ViBrism DB
  • URL: http://vibrism.neuroinf.jp/
• [Remarks] BiVrism-DB
  • URL: http://vibrism.riken.jp/3dviewer/ex/index.html
• [Remarks] rikenchannel: mapping gnes onto brain structures
  • URL: http://www.youtube.com/watch?v=Td4rGRQIZuY&list=UUIGmhpdcVev1Wc0YK7FHIig
• [Remarks] rikenchannel: 遺伝子を脳構造にマップする
  • URL: http://www.youtube.com/watch?v=3a951otikWs&list=UUIGmhpdcVev1Wc0YK7FHIig