Research Clusters

Digital Plant Cell Biology

Research Keyword: Bioimage Analysis, Cytoskeleton, Organelle

With the recent advances in bioimaging equipment such as microscopes, information processing of bioimages is attracting attention as a new research field in bioinformatics. In the IROAST Research Cluster "Digital Plant Cell Biology," we will develop and validate microscopic image analysis techniques to quantitatively evaluate the dynamics of intracellular structures in plant cells. In particular, we will develop biological image analysis frameworks that quantitatively assess the multidimensional biological features of cytoskeleton, and utilize machine learning to make biological discoveries.

Digital Plant Cell Biology

Cluster members

  • Japan
    Takumi HIGAKI Website
    Professor, Faculty of Advanced Science and Technology (FAST), Kumamoto University
  • U.S.A.
    Bo LIU Website
    Professor/ IROAST Visiting Professor, University of California at Davis
  • Japan
    Kae AKITA Website
    Lecturer, Nihon University



 Ezaki K, Koga H, Takeda-Kamiya N, Toyooka K, Higaki T, Sakamoto S, Tsukaya H(2024) Precocious cell differentiation occurs in proliferating cells in leaf primordia in Arabidopsis angustifolia3 mutant Front Plant Sci 15: 1322223

Yuki Hitora, Ahmed H. El-Desoky, Yusaku Sadahiro, Ai Sejiyama, Amiri Kinoshita, Yuji Ise, Esther D. Angkouw, Remy E. P. Mangindaan, Takumi Higaki, and Sachiko Tsukamoto*

Ichita M, Higaki T (2023) Intracellular trafficking regulation of plasma membrane H+-ATPase and environmental response in plants. Cytologia 88: 169-173. (Published: 27 Sep 2023)

Kikukawa K, Takigawa-Imamura H, Soga K, Kotake T, Higaki T (2023) Smooth elongation of pavement cells induced by RIC1 overexpression leads to marginal protrusions of the cotyledon in Arabidopsis thaliana. Plant Cell Physiol. 64(11), 1356-1371. (Published 18 Sep)

Hirano T, Ebine K, Ueda T, Higaki T, Watanabe-Nakayama T, Konno H, Takigawa-Imamura H, Sato MH (2023) The SYP123-VAMP727 SNARE complex delivers secondary cell wall components for root hair shank hardening in Arabidopsis. Plant Cell. 35(12), 4347-4365. (Published 15 Sep 2023)

Yue Y, Hotta T, Higaki T, Verhey KJ, Ohi R (2023) Microtubule detyrosination by VASH1/SVBP is regulated by the conformational state of tubulin in the lattice. Curr Biol 33(19) 4111-4123. (Published 15 Sep 2023)

Matsumoto T, Higaki T, Takatsuka H, Kutsuna N, Ogata Y, Hasezawa S, Umeda M, Inada N (2023) Arabidopsis thaliana subclass I ACTIN DEPOLYMERIZING FACTORs regulate nuclear organization and gene expression. Plant Cell Physiol 64(10), 1231-1242. (Published: 18 Aug 2023)

Takeshi Nishimura, Shogo Mori, Hiromasa Shikata, Moritaka Nakamura, Yasuko Hashiguchi, Yoshinori Abe, Takuma Hagihara, Hiroshi Y. Yoshikawa, Masatsugu Toyota, Takumi Higaki, Miyo Terao Morita (2023) Cell polarity linked to gravity sensing is generated by LZY translocation from statoliths to the plasma membrane Science,  381 (6661) 1006-1010 (Published 10 Aug. 2023)  *press release on August 10, 2023

T Wint H, Li J, Abe T, Yamada H, Higaki T, Nasu Y, Watanabe M, Takei K, Takeda T (2023) Pacsin 2-dependent N-cadherin internalization regulates the migration behaviour of malignant cancer cells. J Cell Sci. 136: 10, jcs.260827. (Published: 3 May 2023)

Takatsuka H, Higaki T, Ito M (2023) At the nexus between cytoskeleton and vacuole: How plant cytoskeletons govern the dynamics of large vacuoles. Int J Mol Sci 24: 4143.

Morotomi-Yano K, Hiromoto Y, Higaki T, Yano KI (2022) Disease-associated H58Y mutation affects the nuclear dynamics of human DNA topoisomerase IIβ. Sci Rep 12: 20627.

Yoshida D, Akita K, Higaki T (2022) Machine learning and feature analysis of the cortical microtubule organization of Arabidopsis cotyledon pavement cells. Protoplasma 260, 987-998.

Hotta T, McAlear TS, Yue Y, Higaki T, Haynes SE, Nesvizhskii AI, Sept D, Verhey KJ, Bechstedt S, Ohi R (2022) EML2-S constitutes a new class of proteins that recognizes and regulates the dynamics of tyrosinated microtubules. Curr Biol. 32, 18, 3898-3910.e14.

Takihara Y, Higaki T, Yokomizo T, Umemoto T, Ariyoshi K, Hashimoto M, Sezaki M, Takizawa H, Inoue T, Suda T, Mizuno H (2022) Bone marrow imaging reveals the migration dynamics of neonatal hematopoietic stem cells. Commun Biol. 5, 776.
*This is a result of the IRCMS-IROAST Joint Research Group, in collaboration with Dr. Mizuno and others at IRCMS, as well.

Sakamoto T, Sakamoto Y, Grob S, Slane D, Yamashita T, Ito N, Oko Y, Sugiyama T, Higaki T, Hasezawa S, Tanaka M, Matsui A, Seki M, Suzuki T, Grossniklaus U, Matsunaga S (2022) Two-step regulation of centromere distribution by condensin II and the nuclear envelope proteins. Nat Plants, 8, 940-953.

Hotta T, Lee YR, Higaki T, Hashimoto T, Liu B (2022) Two Kinesin-14A motors oligomerize to drive poleward microtubule convergence for acentrosomal spindle morphogenesis in Arabidopsis thaliana. Front Cell Dev Biol. 10:949345. 


Takumi Higaki, Grant-in-Aid for Transformative Research Areas (The Japan Society for the Promotion of Science), Platforms for Advanced Technologies and Research Resources "Advanced Bioimaging Support," "Image Analysis Support," April 2022-March 2028.

Takumi Higaki (Lead Joint Researcher), CREST (Japan Science and Technology Agency), Development of technology platforms for quantitative analysis of spatiotemporal multicellular interaction, "Development of novel research strategy that integrates low-dimensionalized bioinformation with multilevel modeling," October 2021-March 2027.

Takumi Higaki, Grant-in-Aid for Scientific Research (B) (The Japan Society for the Promotion of Science), "Multi-dimensional bioimage analyses with machine learning to reveal the dynamics of membrane vesicles and microtubules in stomatal guard cells," April 2020-March 2023.


  • The International Microscopy Congress (IMC20) at BEXCO in Busan, South Korea *Invited lecture 
    Title: "Quantitative evaluation of cytoskeleton organization using fluorescence microscopic image analysis."


  • The International Symposium on "Plant-Structure-Optimization" in Nara -Nov 19-20, 2022-


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