Updated on 2022/07/09


Yoshitaka Kimori


  • PhD   Coursework ( 2006.9   Kyushu Institute of Technology )

Research Areas

  • Informatics / Intelligent robotics

  • Informatics / Perceptual information processing

  • Life Science / Medical systems


  • Kyushu Institute of Technology   Departmemt of Bioscience and Bioinformatics   Graduated

    1997.4 - 2001.3

  • Kyushu Institute of Technology   Master's Course   Completed

    2001.4 - 2003.3

  • Kyushu Institute of Technology   Major of Computer Science and Systems Engineering   Doctor's Course   Accomplished credits for doctoral program

    2003.4 - 2006.3

Research History

  • The University of Tokyo

    2006.4 - 2006.9

  • The University of Tokyo   The institute of medical science

    2006.10 - 2008.7

  • National center of neurology and psychiatry   National institute of Neuroscience   Researcher

    2008.8 - 2010.3

  • National institutes of natural sciences Center for Novel Science Initiatives

    2010.4 - 2011.9

  • National institutes of natural sciences Center for Novel Science Initiatives   Specially appointed assistant professor

    2011.10 - 2018.3

  • Fukui University of Technology   Associate Professor

    2018.4 - 2021.3

  • Fukui University of Technology   Professor


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Professional Memberships

  • IEEE



  • A Morphological Image Preprocessing Method Based on the Geometrical Shape of Lesions to Improve the Lesion Recognition Performance of Convolutional Neural Networks Reviewed International journal

    Yoshitaka Kimori

    IEEE Access   2022.6

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    Convolutional neural networks (CNNs) play an important role in computer vision-related tasks for medical imaging. However, the quality of raw images in the dataset can be insufficient for the CNN model to learn the features of the target object. When the input image contains a complex background, the CNN model focuses on regions that are not essential for lesion recognition, such as background structures, leading to less accurate output prediction. This paper shows that this problem can be efficiently solved by an image preprocessing method based on mathematical morphology, which uses a priori knowledge about the lesion shape. The proposed method consists of h-dome transformation based on the geometrical shape information of the lesion region, and subsequent image histogram-modification processes, and has the ability to selectively enhance the lesion region from the background. This allows for the creation of images that explicitly represent the important region to be learned by the CNN model. Experiments on pulmonary nodule classification in chest x-ray images and skin lesion-region segmentation in dermatoscopic images demonstrate that the CNN models trained on the preprocessed dataset created by the proposed method achieve remarkable performance improvements compared to the CNN models trained on the original dataset.

  • Thermosensitive TRPV4 channels mediate temperature-dependent microglia movement Reviewed

    Rei Nishimoto, Sandra Derouiche, Kei Eto, Aykut Deveci, Makiko Kashio, Yoshitaka Kimori, Yoshikazu Matsuoka, Hiroshi Morimatsu, Junichi Nabekura, Makoto Tominaga

    Proceedings of the National Academy of Sciences   118 ( 17 )   e201289411   2021.4

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    Microglia maintain central nervous system homeostasis by monitoring changes in their environment (resting state) and by taking protective actions to equilibrate such changes (activated state). These surveillance and protective roles both require constant movement of microglia. Interestingly, induced hypothermia can reduce microglia migration caused by ischemia, suggesting that microglia movement can be modulated by temperature. Although several ion channels and transporters are known to support microglia movement, the precise molecular mechanism that regulates temperaturedependent movement of microglia remains unclear. Some members of the transient receptor potential (TRP) channel superfamily exhibit thermosensitivity and thus are strong candidates for mediation of this phenomenon. Here, we demonstrate that mouse microglia exhibit temperature-dependent movement in vitro and in vivo that is mediated by TRPV4 channels within the physiological range of body temperature. Our findings may provide a basis for future research into the potential clinical application of temperature regulation to preserve cell function via manipulation of ion channel activity.

  • Dynamic Capture-and-Release of Endoplasmic Reticulum Exit Sites by Golgi Stacks in Arabidopsis Reviewed

    Junpei Takagi, Yoshitaka Kimori, Tomoo Shimada, Ikuko Hara-Nishimura

    iScience   23 ( 7 )   101265   2020.7

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    小胞体(ER: endoplasmic reticulum)からゴルジ体へのタンパク質輸送は,ER上のER exit site(ERES)と呼ばれる領域に集積しているCOPII小胞が担っている.しかし,ERESとゴルジ体との動的な関連様式はこれまで不明であった.本研究は,シロイヌナズナのゴルジ体におけるERESの動的な捕捉・放出モデルを提案したものである.高時間分解能イメージングにより撮影された細胞試料の顕微鏡像を対象として,ER,ERES,COPII等の解析対象領域を抽出する画像処理手法を開発し,それらの時間,空間的な関連を解析した.

  • A morphological image processing method to improve the visibility of pulmonary nodules on chest radiographic images. Reviewed

    Yoshitaka Kimori

    Biomedical Signal Processing and Control   57   101744   2020.3

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     本研究では,mathematical morphologyを用いた新規の画像処理手法を開発し,複雑な背景の中から,肺結節影のみを特異的に強調することに成功した.

  • Noninvasive measurement of cell/colony motion using image analysis methods to evaluate the proliferative capacity of oral keratinocytes as a tool for quality control in regenerative medicine. Reviewed

    Emi Hoshikawa, Taisuke Sato, Yoshitaka Kimori, Ayako Suzuki, Kenta Haga, Hiroko Kato, Koichi Tabeta, Daisuke Nanba, Kenji Izumi

    Journal of tissue engineering   10   2041731419881528   2019.10

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  • A Method for Evaluating Three-Dimensional Morphological Features: A Case Study Using Marchantia polymorpha Reviewed

    Tomoyuki Furuya, Yoshitaka Kimori, Hirokazu Tsukaya

    Frontiers in plant science   10   1214   2019.10

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    共同研究者として,X線マイクロトモグラフィ技術によって得られたゼニゴケ3次元データに対し,mathematical morphologyに基づく3次元形態特徴の抽出手法の開発を行った.さらにデータ可視化および統計的形態解析手法の開発も行った.

  • Autophagy controls reactive oxygen species homeostasis in guard cells that is essential for stomatal opening. Reviewed

    Shota Yamauchi, Shoji Mano, Kazusato Oikawa, Kazumi Hikino, Kosuke M Teshima, Yoshitaka Kimori, Mikio Nishimura, Ken-ichiro Shimazaki, Atsushi Takemiya

    Proceedings of the National Academy of Sciences   116 ( 38 )   19187 - 19192   2019.9

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  • Heterogeneous distribution of doublecortin‐expressing cells surrounding the rostral migratory stream in the juvenile mouse Reviewed

    Yuka Aoyagi, Terumasa Hibi, Yoshitaka Kimori, Masato Sawada, Ryosuke Kawakami, Kazunobu Sawamoto, Tomomi Nemoto

    Journal of Comparative Neurology   526 ( 16 )   2631 - 2646   2018.11

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    哺乳類の脳において,ニューロンは脳室下帯と海馬歯状回の2か所の領域に存在する神経幹細胞から,生涯を通じ新生する.特に,脳室下帯において新生したニューロンは移動能を有しておりrostral migratory stream(RMS)と呼ばれる経路に沿って嗅球に移動したのち,成熟したニューロンとして供給される.しかし,これまで,RMSに沿った移動に関する,新生ニューロンの3次元的な空間分布の詳細は不明であった.本研究では,2光子顕微鏡を用い,マウスの脳組織の3次元構造を撮影することにより,移動する新生ニューロンの空間分布の解析を行った.

  • Endoplasmic Reticulum (ER) Membrane Proteins (LUNAPARKs) are Required for Proper Configuration of the Cortical ER Network in Plant Cells Reviewed

    Haruko Ueda, Natsumi Ohta, Yoshitaka Kimori, Teruka Uchida, Tomoo Shimada, Kentaro Tamura, Ikuko Hara-Nishimura

    Plant and Cell Physiology   59 ( 10 )   1931 - 1941   2018.10

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  • Length of myelin internodes of individual oligodendrocytes is controlled by microenvironment influenced by normal and input‐deprived axonal activities in sensory deprived mouse models Reviewed

    Yasuyuki Osanai, Takeshi Shimizu, Takuma Mori, Nobuhiko Hatanaka, Yoshitaka Kimori, Kenta Kobayashi, Shinsuke Koyama, Yumiko Yoshimura, Atsushi Nambu, Kazuhiro Ikenaka

    Glia   66 ( 11 )   2514 - 2525   2018.9

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    本研究は,脳に分布するグリア細胞の一種である,オリゴデンドロサイト(稀突起グリア細胞)の髄鞘形成メカニズムを解明したものである.その機能を解明するためには,髄鞘構造に関する詳細な情報が必要であるが,顕微鏡を用いた観察では困難であった. 本研究では,蛍光顕微鏡像によって取得されたオリゴデンドロサイトの3Dデータに基づき,その髄鞘構造の可視化を実施し,機能発現機構の詳細を調べた.

  • ANGUSTIFOLIA contributes to the regulation of three-dimensional morphogenesis in the liverwort Marchantia polymorpha Reviewed

    Tomoyuki Furuya, Koro Hattori, Yoshitaka Kimori, Sakiko Ishida, Ryuichi Nishihama, Takayuki Kohchi, Hirokazu Tsukaya

    Development   145 ( 18 )   dev161398   2018.9

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  • Implications of maintenance of mother-bud neck size in diverse vital processes of Saccharomyces cerevisiae Reviewed

    Current Genetics   1 - 15   2018.7

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    真核細胞のモデル系である出芽酵母では,ポストゲノム時代を迎えてフェノーム研究(表現型の網羅的研究)が盛んに行なわれるようになり,研究者の目に頼らない画像解析システムの開発の必要性が高まってきた.本手法では,大容量の画像中から酵母の領域を自動で検出し,母細胞から出芽する娘細胞の境界(bud neck)のサイズを定量的に記述する手法を開発し,そのサイズの維持が増殖等の細胞プロセスに重要であることを示した.

  • Different Activity Patterns in Retinal Ganglion Cells of TRPM1 and mGluR6 Knockout Mice Reviewed

    Haruki Takeuchi, Sho Horie, Satoru Moritoh, Hiroki Matsushima, Tesshu Hori, Yoshitaka Kimori, Katsunori Kitano, Yasuhiro Tsubo, Masao Tachibana, Chieko Koike

    BioMed Research International   2963232   2018.5

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    感覚受容に関わるTRP(transient receptor potential)familyの1つであるTRPM1は網膜に強く発現しており,ヒトTRPM1遺伝子の変異が完全型停止性夜盲症の原因になっていることが知られている.また,TRPM1は,網膜ON型双極細胞の樹状突起において,mGluR
    6(代謝型グルタミン酸受容体6)と共局在することが分かっている.本研究では,TRMP1とmGluR6ノックアウト(KO)マウスの網膜桿体ON型双極細胞の神経終末の構造解析を行い,TRMP1 KO網膜では,mGluR KO網膜よりもシナプス終末のサイズは有意に小さいことを見出した.このことは,桿体ON型双極細胞においては,mGluR6ではなく,TRMP1の欠損がシナプス終末の制術に影響を及ぼしていることを示唆している.

  • YTH-RNA-binding protein prevents deleterious expression of meiotic proteins by tethering their mRNAs to nuclear foci Reviewed

    Yuichi Shichino, Yoko Otsubo, Yoshitaka Kimori, Masayuki Yamamoto, Akira Yamashita

    eLife   7   e32155   2018.2

  • Rabies Virus‐Mediated Oligodendrocyte Labeling Reveals A Single Oligodendrocyte Myelinates Axons from Distinct Brain Regions Reviewed

    Yasuyuki Osanai, Takeshi Shimizu, Takuma Mori, Yumiko Yoshimura, Nobuhiko Hatanaka, Atsushi Nambu, Yoshitaka Kimori, Shinsuke Koyama, Kenta Kobayashi, Kazuhiro Ikenaka

    Glia   65   93 - 105   2017.1

  • Ultrastructure of Compacted DNA in Cyanobacteria by High-Voltage Cryo-Electron Tomography Reviewed

    Kazuyoshi Murata, Sayuri Hagiwara, Yoshitaka Kimori, Yasuko Kaneko

    Scientific Reports   6   34934   2016.10

  • Quantifying Morphological Features of Actin Cytoskeletal Filaments in Plant Cells Based on Mathematical Morphology Reviewed

    Yoshitaka Kimori, Kazumi Hikino, Mikio Nishimura, Shoji Mano

    Journal of Theoretical Biology   389   123 - 131   2016.1

  • Irradiation-injured Brain Tissues Can Self-Renew in The Absence of The Pivotal Tumor Suppressor p53 in The Medaka (Oryzias latipes) Embryo Reviewed

    Takako Yasuda, Yoshitaka Kimori, Kento Nagata, Kento Igarashi, Tomomi Watanabe-Asaka, Shoji Oda, Hiroshi Mitani

    Journal of Radiation Research   57   9 - 15   2016.1

  • Single-Cell Phenomics in Budding Yeast Reviewed

    Yoshikazu Ohya, Yoshitaka Kimori, Hiroki Okada, Shinsuke Ohnuki

    Molecular Biology of the Cell   26   3920 - 3925   2015.11

  • Morphological Image Processing for Quantitative Shape Analysis of Biomedical Structures: Effective Contrast Enhancement Reviewed

    Yoshitaka Kimori

    Journal of Synchrotron Radiation   20   848 - 853   2013.11

  • Novel Configuration of A Myosin II Transient Intermediate Analogue Revealed by Quick-Freeze Deep-Etch Replica Electron Microscopy Reviewed

    Yoshitaka KIMORI, Norio BABA, Eisaku KATAYAMA

    Biochemical Journal   450   23 - 35   2013.2

  • Gamma-ray irradiation promotes premature meiosis of spontaneously differentiating testis-ova in the testis of p53 deficient medaka (Oryzias latipes) Reviewed

    T Yasuda, S Oda, Z Li, Y Kimori, Y Kamei, T Ishikawa, T Todo, H Mitani

    Cell Death and Disease   3   e395   2012.10

  • Mathematical Morphology-based Approach to the Enhancement of Morphological Features in Medical Images Reviewed

    Yoshitaka Kimori

    Journal of Clinical Bioinformatics   1   33   2011.12

  • Myostatin-deficient medaka Exhibit a Double-muscling Phenotype with Hyperplasia and Hypertrophy, which Occur Sequentially During Post-hatch Development Reviewed

    Shin-ichi Chisada, Hiroyuki Okamoto, Yoshihito Taniguchi, Yoshitaka Kimori, Atsushi Toyoda, Yoshiyuki Sakaki, Shunichi Takeda, Yasutoshi Yoshiura

    Developmental Biology   359   82 - 94   2011.11

  • Fractal Dimension Analysis and Mathematical Morphology of Structural Changes in Actin Filaments Imaged by Electron Microscopy Reviewed

    Yoshitaka Kimori, Eisaku Katayama, Nobuhiro Morone, Takao Kodama

    Journal of Structural Biology   176   1 - 8   2011.10

  • Extended Morphological Processing: A Practical Method for Automatic Spot Detection of Biological Markers from Microscopic Images Reviewed

    Yoshitaka Kimori, Norio Baba, Nobuhiro Morone

    BMC Bioinformatics   11   373   2010.7

  • Procedure to Analyze Surface Profiles of the Protein Molecules Visualized by Quick-Freeze Deep-Etch Replica Electron Microscopy Reviewed

    Yoshitaka Kimori, Yosuke Oguchi, Norihiko Ichise, Norio Baba, Eisaku Katayama

    Ultramicroscopy   107   25 - 39   2007.1

  • Aggregation of Partially Unfolded Myosin Subfragment-1 into Spherical Oligomers with Amyloid-Like Dye-Binding Properties Reviewed

    Hideyuki Komatsu, Nami Shinotani, Yoshitaka Kimori, Jun-ichiro Tokuoka, Kuniyoshi Kaseda, Hiroyuki Nakagawa, Takao Kodama

    Journal of Biochemistry   139   989 - 996   2006.6

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  • Using image-based resources: databases for plant organelle dynamics, and applications based on image information, In Introduction to Sequence and Genome Analysis I

    Mano S., Kimori Y., Takeda T., Miwa T., Nishikawa S., Mimura T.( Role: Joint author ,  第3章「Morphological Image Processing for the Quantitative Analysis of Biological Images」, pp. 90-99.)

    iConcept Press  2013.7 


  • Quantitative measurement of mobility of cell colony using image analysis methods for quality control of oral keratinocytes: A preliminary study International conference

    Hoshikawa E., Kimori Y., Sato T., Kato H., Suzuki A., Haga K., Nanba D., Izumi K.

    5th Tissue Engineering and Regenerative Medicine International Society World Congress  Tissue Engineering and Regenerative Medicine International Society

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