Tatsuya Murakami

Publications

2025

Curved Axially Scanned Light-Sheet Microscopy
Steven J. Sheppard, Tatsuya C. Murakami, Douglas P. Shepherd
openRxiv  ·  09 Dec 2025  ·  doi:10.64898/2025.12.03.691599
An open-source photobleacher for fluorescence imaging of large pigment-rich tissues
Tatsuya C. Murakami, Nick Belenko, Griffin Dennis, Cuidong Wang, Maria Esterlita Siantoputri, Yurie Maeda, Christina Pressl, Nathaniel Heintz
Proceedings of the National Academy of Sciences  ·  17 Sep 2025  ·  doi:10.1073/pnas.2426628122
Artificial Intelligence-driven Whole-brain Cell Mapping with Highly Multiplexed In Situ Hybridization
Tatsuya Murakami, Meng Xia, Yurie Maeda, Yuejia Yin, Paolo Emilio Barbano, Ziyi Lin, Tomoyuki Mano, Kazuki Tainaka, Sam Reiter, Nathaniel Heintz
BioRxiv  ·  22 Aug 2025  ·  doi:10.1101/2025.08.18.670857

2024

Precise 3D Localization of Intracerebral Implants Using a Simple Brain Clearing Method
Julien Catanese, Tatsuya C. Murakami, Adam Catto, Paul J. Kenny, Ines Ibañez-Tallon
Journal of Integrative Neuroscience  ·  20 Nov 2024  ·  doi:10.31083/j.jin2311207
Spontaneously regenerative corticospinal neurons in mice
Benjamin W Fait, Bianca Cotto, Tatsuya C. Murakami, Michael Hagemann-Jensen, Huiqing Zhan, …, Hongkui Zeng, Bosiljka Tasic, Oswald Steward, Nathaniel Heintz, Eric F Schmidt
BioRxiv  ·  12 Sep 2024  ·  doi:10.1101/2024.09.09.612115

2022

Multiplexed and scalable cellular phenotyping toward the standardized three-dimensional human neuroanatomy
Tatsuya C. Murakami, Nathaniel Heintz
BioRxiv  ·  24 Nov 2022  ·  doi:10.1101/2022.11.23.517711

2019

Advanced CUBIC tissue clearing for whole-organ cell profiling
Katsuhiko Matsumoto, Tomoki T. Mitani, Shuhei A. Horiguchi, Junichi Kaneshiro, Tatsuya C. Murakami, …, Hiroshi Fujishima, Ayumu Konno, Tomonobu M. Watanabe, Hirokazu Hirai, Hiroki R. Ueda
Nature Protocols  ·  20 Nov 2019  ·  doi:10.1038/s41596-019-0240-9

2018

Chemical Landscape for Tissue Clearing Based on Hydrophilic Reagents
Kazuki Tainaka, Tatsuya C. Murakami, Etsuo A. Susaki, Chika Shimizu, Rie Saito, …, Eiichi Morii, Tadashi Isa, Masashi Fukayama, Akiyoshi Kakita, Hiroki R. Ueda
Cell Reports  ·  01 Aug 2018  ·  doi:10.1016/j.celrep.2018.07.056
A three-dimensional single-cell-resolution whole-brain atlas using CUBIC-X expansion microscopy and tissue clearing
Tatsuya C. Murakami, Tomoyuki Mano, Shu Saikawa, Shuhei A. Horiguchi, Daichi Shigeta, …, Hiroshi Kiyonari, Masamitsu Iino, Hideki Mochizuki, Kazuki Tainaka, Hiroki R. Ueda
Nature Neuroscience  ·  05 Mar 2018  ·  doi:10.1038/s41593-018-0109-1

2016

Chemical Principles in Tissue Clearing and Staining Protocols for Whole-Body Cell Profiling
Kazuki Tainaka, Akihiro Kuno, Shimpei I. Kubota, Tatzya Murakami, Hiroki R. Ueda
Annual Review of Cell and Developmental Biology  ·  06 Oct 2016  ·  doi:10.1146/annurev-cellbio-111315-125001

2015

Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae
Dong Yan, Yun Wang, Tatsuya Murakami, Yue Shen, Jianhui Gong, Huifeng Jiang, David R. Smith, Jean-Francois Pombert, Junbiao Dai, Qingyu Wu
Scientific Reports  ·  25 Sep 2015  ·  doi:10.1038/srep14465