Publications

2026

Artificial intelligence-driven whole-brain cell mapping with highly multiplexed in situ hybridization

Tatsuya C. Murakami, Meng Xia, Yurie Maeda, Yuejia Yin, Paolo Emilio Barbano, Ziyi Lin, Tomoyuki Mano, Kazuki Tainaka, Sam Reiter, Nathaniel Heintz

Neuron · 01 Apr 2026 · doi:10.1016/j.neuron.2025.12.027

Curved axially scanned light-sheet microscopy

Steven J. Sheppard, Tatsuya C. Murakami, Douglas P. Shepherd

Optica · 30 Mar 2026 · doi:10.1364/optica.586764

2025

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

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