Author

Tatsuya C. Murakami

Rockefeller UniversityORCID 0000-0002-3734-9359Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

Click to filter author papers

Signature Assays, Organisms & Methods

Click to filter · or open tag

Approach:experimental assay· 6 Organism:human· 4 Assay:imaging· 3 Organism:mouse· 3 Research Focus:cell type annotation· 2 Research Focus:clustering· 2 Research Focus:spatial domain detection· 2 Assay:spatial transcriptomics· 2

Frequent Co-Authors

Nathaniel HeintziD· 5 shared Yurie Maeda· 2 shared Benjamin W. FaitiD· 1 shared Bianca CottoiD· 1 shared Bosiljka TasiciD· 1 shared Christina PressliD· 1 shared Corinne Freivald· 1 shared Cuidong WangiD· 1 shared

Activity by Year

2022-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 21 mutual co-author links

Click any collaborator node to inspect or filter shared papers

Focal author (center)Selected co-authorORCID co-authorUnlinked name

Curved chords = mutual co-authorship

5 shared papersNeuroscience

Nathaniel HeintzORCID

Mutual co-authors in cluster

Author profile →

7 papers

Recent·Most cited

Reconstructing the developmental history of the cortex from postmortem tissue

Tatsuya C. Murakami, Nathaniel Heintz

This paper reconstructs the developmental history of the cortex from postmortem tissue by analyzing cell distribution and estimating stem cell proliferation rates.

bioRxiv · Jul 22, 2026 · PreprintNeuroscience

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

The paper introduces mFISH3D, a multiplexed staining technique combined with AI for high-resolution whole-brain cell mapping in mice and humans.

Neuron · Feb 18, 2026Peer-reviewedNeuroscience

Curved Axially Scanned Light-Sheet Microscopy

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

The paper introduces curved axially scanned light-sheet microscopy to overcome field curvature limitations in light-sheet imaging, increasing the usable field of view while maintaining sub-cellular resolution.

Optica · Feb 10, 2026Peer-reviewedBiophysics

Open-source Photobleacher for Fluorescent Imaging of Large Pigment-Rich Tissues

Tatsuya C. Murakami, Nick Belenko, Griffin Dennis, Cuidong Wang, Maria Esterlita Siantoputri, Yurie Maeda, Christina Pressl, Nathaniel Heintz

The paper introduces an open-source photobleacher to quench endogenous pigments in tissues, enabling high-contrast fluorescent imaging for multiplexed molecular analysis.

bioRxiv · Feb 24, 2025 · PreprintNeuroscience

Spontaneously regenerative corticospinal neurons in mice

Benjamin W. Fait, Bianca Cotto, Tatsuya C. Murakami, Michael Hagemann-Jensen, Huiqing Zhan, Corinne Freivald, Isadora Turbek, Yuan Gao, Zizhen Yao, Sharon W. Way, Hongkui Zeng, Bosiljka Tasic, Oswald Steward, Nathaniel Heintz, Eric F. Schmidt

The paper identifies a class of spontaneously regenerative corticospinal neurons in mice that project ipsilaterally and share molecular features with embryonic-like regenerating neurons.

bioRxiv · Sep 9, 2024 · PreprintNeuroscience

Precise 3D Localization of Intracerebral Implants with a simple Brain Clearing Method

Julien Catanese, Tatsuya C. Murakami, Paul J. Kenny, Inés Ibáñez-Tallon

The paper introduces a method for precise 3D localization of intracerebral implants in rodent brains using tissue-clearing and light-sheet fluorescence microscopy, demonstrating its utility with implantation examples in transgenic mice.

bioRxiv · Dec 22, 2023 · PreprintNeuroscience

Multiplexed and scalable cellular phenotyping toward the standardized three-dimensional human neuroanatomy

Tatsuya C. Murakami, Nathaniel Heintz

The paper introduces a scalable staining/imaging technique for single-cell-resolution mRNA analysis in human brains and applies it to quantify cortical cytoarchitecture.

bioRxiv · Nov 23, 2022 · PreprintNeuroscience