Basic Information

Email Address

• Email Address

  gong.rui.6fkyoto-u.ac.jp

Academic Degree

• 11 May 2018

  Ph.D.（The University of Auckland）
• 02 May 2012

  M.S.（The University of Auckland）

Academic Resume (Graduate Schools)

• The University of Auckland, Faculty of Science，Department of Computer Science，Doctoral Study, 修了
• The University of Auckland, Faculty of Science，Department of Computer Science，Masters Study, 修了
• The University of Auckland, Faculty of Science，Department of Computer Science，Postgraduate Diploma, 修了

Academic Resume (Undergraduate School/Majors)

• The University of Auckland, Faculty of Science，Department of Computer Science，Bachelor of Science, 卒業

Language of Instruction

• English
• Chinese
• Japanese

ID,URL

• ORCID ID

  0000-0001-8197-0460

• Researcher number

  10813686

researchmap URL

• https://researchmap.jp/ruigong

Research

Research Areas

• Informatics, Computational science

Papers

• Template-Based Label Propagation for Mouse Brain MRI Skull Stripping

  Rui Gong; Andrii Gegliuk; Daria Sharapova; Bhanu Sharma; Yoshifumi Abe; Ken Nakae; Shin Ishii; Sho Yagishita

  Neuroinformatics, 01 May 2026, Lead author

  
• Brain/MINDS Marmoset Brain Atlas 2.0: Population Cortical Parcellation With Multi-Modal Templates

  Rui Gong; Noritaka Ichinohe; Hiroshi Abe; Toshiki Tani; Mengkuan Lin; Takuto Okuno; Ken Nakae; Junichi Hata; Shin Ishii; Patrice Delmas; Shahrokh Heidari; Jiaxuan Wang; Tetsuo Yamamori; Hideyuki Okano; Alexander Woodward

  Scientific Data, 16 Jan. 2026, Lead author

  
• A Deep Learning-based Pipeline for Segmenting the Cerebral Cortex Laminar Structure in Histology Images

  Wang, J.; Gong, R.; Heidari, S.; Rogers, M.; Tani, T.; Abe, H.; Ichinohe, N.; Woodward, A.; Delmas, P.J.

  Neuroinformatics, 17 Oct. 2024

  
• Commonality and variance of resting-state networks in common marmoset brains

  Muta, K.; Haga, Y.; Hata, J.; Kaneko, T.; Hagiya, K.; Komaki, Y.; Seki, F.; Yoshimaru, D.; Nakae, K.; Woodward, A.; Gong, R.; Kishi, N.; Okano, H.

  Scientific Reports, 09 Apr. 2024

  
• Local and long-distance organization of prefrontal cortex circuits in the marmoset brain

  Akiya Watakabe; Henrik Skibbe; Ken Nakae; Hiroshi Abe; Noritaka Ichinohe; Muhammad Febrian Rachmadi; Jian Wang; Masafumi Takaji; Hiroaki Mizukami; Alexander Woodward; Rui Gong; Junichi Hata; David C. Van Essen; Hideyuki Okano; Shin Ishii; Tetsuo Yamamori

  Neuron, Jul. 2023

  
• Multi-modal brain magnetic resonance imaging database covering marmosets with a wide age range

  Junichi Hata; Ken Nakae; Hiromichi Tsukada; Alexander Woodward; Yawara Haga; Mayu Iida; Akiko Uematsu; Fumiko Seki; Noritaka Ichinohe; Rui Gong; Takaaki Kaneko; Daisuke Yoshimaru; Akiya Watakabe; Hiroshi Abe; Toshiki Tani; Hiro Taiyo Hamda; Carlos Enrique Gutierrez; Henrik Skibbe; Masahide Maeda; Frederic Papazian; Kei Hagiya; Noriyuki Kishi; Shin Ishii; Kenji Doya; Tomomi Shimogori; Tetsuo Yamamori; Keiji Tanaka; Hirotaka James Okano; Hideyuki Okano

  Scientific Data, 27 Apr. 2023

  
• A 2D Cortical Flat Map Space for Computationally Efficient Mammalian Brain Simulation

  Alexander Woodward; Rui Gong; Ken Nakae; Patrice Delmas

  Lecture Notes in Computer Science, 2023

  
• The NanoZoomer Connectomics Pipeline for Tracer Injection Studies of the Marmoset Brain

  Woodward, Alexander; Gong, Rui; Abe, Hiroshi; Nakae, Ken; Hata, Junichi; Skibbe, Henrik; Yamaguchi, Yoko; Ishii, Shin; Okano, Hideyuki; Yamamori; Tetsuo

  bioRxiv, 2019

  
• MarmoNet: a pipeline for automated projection mapping of the common marmoset brain from whole-brain serial two-photon tomography

  Skibbe, Henrik; Watakabe, Akiya; Nakae, Ken; Gutierrez; Carlos Enrique; Tsukada, Hiromichi; Hata, Junichi; Kawase, Takashi; Gong, Rui; Woodward; Alexander a; Doya; Kenji and

  arXiv preprint arXiv:1908.00876, 2019

  
• Robust Tracking in Weakly Dynamic Scenes

  Trevor Gee; Rui Gong; Patrice Delmas; Georgy Gimel’farb

  Lecture Notes in Computer Science, 23 Nov. 2017

  
• A low cost framework for real-time marker based 3-D human expression modeling

  Woodward, A.; Chan, Y.H.; Gong, R.; Nguyen, M.; Gee, T.; Delmas, P.; Gimel{'}farb, G.; Marquez Flores, J.A.

  Journal of Applied Research and Technology, 2017

  
• Semi-global stereo matching under large and spatially variant perceptive deviations

  Rui Gong; Georgy Gimel'farb; Patrice Delmas

  2015 International Conference on Image and Vision Computing New Zealand (IVCNZ), Nov. 2015, Lead author

  
• Toward a real-time belief propagation stereo reconstruction for computers, robots, and beyond

  Minh Nguyen; Wei Qi Yan; Rui Gong; Patrice Delmas

  2015 International Conference on Image and Vision Computing New Zealand (IVCNZ), Nov. 2015

  
• Regularising ill-posed discrete optimisation: Quests with P systems

  Nicolescu, R.; Gimel{'}Farb, G.; Delmas, P.; Gong, R.

  Fundamenta Informaticae, 2014

  
• Multi-Kinect scene reconstruction: Calibration and depth inconsistencies

  Roy Sirui Yang; Yuk Hin Chan; Rui Gong; Minh Nguyen; Alfonso Gastelum Strozzi; Patrice Delmas; Georgy Gimel'farb; Rachel Ababou

  2013 28th International Conference on Image and Vision Computing New Zealand (IVCNZ 2013), Nov. 2013

  
• Towards structural analysis of solution spaces for ill-posed discrete 1D optimisation problems

  Rui Gong; Georgy Gimel'farb; Radu Nicolescu; Patrice Delmas

  2013 28th International Conference on Image and Vision Computing New Zealand (IVCNZ 2013), Nov. 2013, Lead author

  
• Context-driven composite stereo reconstruction

  M. Nguyen; R. Gong; Y.-H. Chan; P. Delmas; G. Gimel'farb

  Proceedings of the 27th Conference on Image and Vision Computing New Zealand, 26 Nov. 2012

  
• The Ngongotaha river UDPS experiment

  Y. H. Chan; M. Nguyen; A. Gastelum; S. Yang; R. Gong; N. Liu; P. Delmas; G. Gimel'farb; S. Bertin; H. Friedrich

  Proceedings of the 27th Conference on Image and Vision Computing New Zealand, 26 Nov. 2012

  
• Modelling of elastic deformation using stereo vision and smoothed particle hydrodynamics

  Yuk Hin Chan; Alfonso Gastelum Strozzi; Anthony Lau; Rui Gong; Patrice Delmas; Georgy Gimel'farb; Jorge Marquez

  2009 24th International Conference Image and Vision Computing New Zealand, Nov. 2009