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Items: 1 to 20 of 1909

1.
Oblique line scan illumination enables expansive, accurate and sensitive single-protein measurements in solution and in living cells
Amine Driouchi, Mason Bretan, Brynmor J. Davis, Alec Heckert, Markus Seeger, Maité Bradley Silva, William S. R. Forrest, Jessica Hsiung, Jiongyi Tan, Hongli Yang, David T. McSwiggen, Linda Song, Askhay Sule, Behnam Abaie, Hanzhe Chen, Bryant Chhun, Brianna Conroy, Liam A. Elliott, Eric Gonzalez, Fedor Ilkov, Joshua Isaacs, George Labaria, Michelle Lagana, DeLaine D. Larsen, Brian Margolin, Mai K. Nguyen, Eugene Park, Jeremy Rine, Yangzhong Tang, Martin Vana, Andrew Wilkey, Zhengjian Zhang, Stephen Basham, Jaclyn J. Ho, Stephanie Johnson, Aaron A. Klammer, Kevin Lin, Xavier Darzacq, Eric Betzig, Russell T. Berman, Daniel J. Anderson
Nat Methods. 2025; 22(3): 559–568. Published online 2025 Feb 18. doi: 10.1038/s41592-025-02594-6
PMCID:
PMC11903300
ArticlePDF–12M
2.
Cellpose3: one-click image restoration for improved cellular segmentation
Carsen Stringer, Marius Pachitariu
Nat Methods. 2025; 22(3): 592–599. Published online 2025 Feb 12. doi: 10.1038/s41592-025-02595-5
PMCID:
PMC11903308
ArticlePDF–18M
3.
DeepPrep: an accelerated, scalable and robust pipeline for neuroimaging preprocessing empowered by deep learning
Jianxun Ren, Ning An, Cong Lin, Youjia Zhang, Zhenyu Sun, Wei Zhang, Shiyi Li, Ning Guo, Weigang Cui, Qingyu Hu, Weiwei Wang, Xuehai Wu, Yinyan Wang, Tao Jiang, Theodore D. Satterthwaite, Danhong Wang, Hesheng Liu
Nat Methods. 2025; 22(3): 473–476. Published online 2025 Feb 6. doi: 10.1038/s41592-025-02599-1
PMCID:
PMC11903312
ArticlePDF–5.8M
4.
A genome-wide atlas of human cell morphology
Meraj Ramezani, Erin Weisbart, Julia Bauman, Avtar Singh, John Yong, Maria Lozada, Gregory P. Way, Sanam L. Kavari, Celeste Diaz, Eddy Leardini, Gunjan Jetley, Jenlu Pagnotta, Marzieh Haghighi, Thiago M. Batista, Joaquín Pérez-Schindler, Melina Claussnitzer, Shantanu Singh, Beth A. Cimini, Paul C. Blainey, Anne E. Carpenter, Calvin H. Jan, James T. Neal
Nat Methods. 2025; 22(3): 621–633. Published online 2025 Jan 27. doi: 10.1038/s41592-024-02537-7
PMCID:
PMC11903339
ArticlePDF–25M
5.
Author Correction: A comprehensive human embryo reference tool using single-cell RNA-sequencing data
Cheng Zhao, Alvaro Plaza Reyes, John Paul Schell, Jere Weltner, Nicolás M. Ortega, Yi Zheng, Åsa K. Björklund, Laura Baqué-Vidal, Joonas Sokka, Ras Trokovic, Brian Cox, Janet Rossant, Jianping Fu, Sophie Petropoulos, Fredrik Lanner
Nat Methods. 2025; 22(3): 636. Published online 2025 Jan 24. doi: 10.1038/s41592-025-02601-w
Corrects:
Nat Methods. 2025; 22(1): 193–206.
PMCID:
PMC11903301
CorrectionPDF–448K
6.
Challenging the Astral mass analyzer to quantify up to 5,300 proteins per single cell at unseen accuracy to uncover cellular heterogeneity
Julia A. Bubis, Tabiwang N. Arrey, Eugen Damoc, Bernard Delanghe, Jana Slovakova, Theresa M. Sommer, Harunobu Kagawa, Peter Pichler, Nicolas Rivron, Karl Mechtler, Manuel Matzinger
Nat Methods. 2025; 22(3): 510–519. Published online 2025 Jan 16. doi: 10.1038/s41592-024-02559-1
PMCID:
PMC11903296
ArticlePDF–3.2M
7.
Orthology inference at scale with FastOMA
Sina Majidian, Yannis Nevers, Ali Yazdizadeh Kharrazi, Alex Warwick Vesztrocy, Stefano Pascarelli, David Moi, Natasha Glover, Adrian M. Altenhoff, Christophe Dessimoz
Nat Methods. 2025; 22(2): 269–272. Published online 2025 Jan 3. doi: 10.1038/s41592-024-02552-8
PMCID:
PMC11810774
ArticlePDF–1.9M
8.
MouseGoggles: an immersive virtual reality headset for mouse neuroscience and behavior
Matthew Isaacson, Hongyu Chang, Laura Berkowitz, Rick Zirkel, Yusol Park, Danyu Hu, Ian Ellwood, Chris B. Schaffer
Nat Methods. 2025; 22(2): 380–385. Published online 2024 Dec 12. doi: 10.1038/s41592-024-02540-y
PMCID:
PMC11810773
ArticlePDF–6.0M
9.
A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs
Caroline Brown, Snehasish Ghosh, Rachel McAllister, Mukesh Kumar, Gerard Walker, Eric Sun, Talat Aman, Aniruddha Panda, Shailesh Kumar, Wenxue Li, Jeff Coleman, Yansheng Liu, James E. Rothman, Moitrayee Bhattacharyya, Kallol Gupta
Nat Methods. 2025; 22(2): 412–421. Published online 2024 Nov 28. doi: 10.1038/s41592-024-02517-x
PMCID:
PMC11810782
ArticlePDF–9.0M
10.
A benchmarked, high-efficiency prime editing platform for multiplexed dropout screening
Ann Cirincione, Danny Simpson, Weihao Yan, Ryan McNulty, Purnima Ravisankar, Sabrina C. Solley, Jun Yan, Fabian Lim, Emma K. Farley, Mona Singh, Britt Adamson
Nat Methods. 2025; 22(1): 92–101. Published online 2024 Nov 19. doi: 10.1038/s41592-024-02502-4
PMCID:
PMC11725502
ArticlePDF–16M
11.
Deep learning-based models for preimplantation mouse and human embryos based on single-cell RNA sequencing
Martin Proks, Nazmus Salehin, Joshua M. Brickman
Nat Methods. 2025; 22(1): 207–216. Published online 2024 Nov 14. doi: 10.1038/s41592-024-02511-3
PMCID:
PMC11725497
ArticlePDF–12M
12.
Analysis of behavioral flow resolves latent phenotypes
Lukas M. von Ziegler, Fabienne K. Roessler, Oliver Sturman, Rebecca Waag, Mattia Privitera, Sian N. Duss, Eoin C. O’Connor, Johannes Bohacek
Nat Methods. 2024; 21(12): 2376–2387. Published online 2024 Nov 12. doi: 10.1038/s41592-024-02500-6
PMCID:
PMC11621029
ArticlePDF–9.5M
13.
ONIX: a unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior
Jonathan P. Newman, Jie Zhang, Aarón Cuevas-López, Nicholas J. Miller, Takato Honda, Marie-Sophie H. van der Goes, Alexandra H. Leighton, Filipe Carvalho, Gonçalo Lopes, Anna Lakunina, Joshua H. Siegle, Mark T. Harnett, Matthew A. Wilson, Jakob Voigts
Nat Methods. 2025; 22(1): 187–192. Published online 2024 Nov 11. doi: 10.1038/s41592-024-02521-1
PMCID:
PMC11725498
ArticlePDF–13M
14.
Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations
Alex R. Lederer, Maxine Leonardi, Lorenzo Talamanca, Daniil M. Bobrovskiy, Antonio Herrera, Colas Droin, Irina Khven, Hugo J. F. Carvalho, Alessandro Valente, Albert Dominguez Mantes, Pau Mulet Arabí, Luca Pinello, Felix Naef, Gioele La Manno
Nat Methods. 2024; 21(12): 2271–2286. Published online 2024 Oct 31. doi: 10.1038/s41592-024-02471-8
PMCID:
PMC11621032
ArticlePDF–18M
15.
Quality control for single-cell analysis of high-plex tissue profiles using CyLinter
Gregory J. Baker, Edward Novikov, Ziyuan Zhao, Tuulia Vallius, Janae A. Davis, Jia-Ren Lin, Jeremy L. Muhlich, Elizabeth A. Mittendorf, Sandro Santagata, Jennifer L. Guerriero, Peter K. Sorger
Nat Methods. 2024; 21(12): 2248–2259. Published online 2024 Oct 30. doi: 10.1038/s41592-024-02328-0
PMCID:
PMC11621021
ArticlePDF–22M
16.
Influence of different sample preparation approaches on proteoform identification by top-down proteomics
Philipp T. Kaulich, Kyowon Jeong, Oliver Kohlbacher, Andreas Tholey
Nat Methods. 2024; 21(12): 2397–2407. Published online 2024 Oct 22. doi: 10.1038/s41592-024-02481-6
PMCID:
PMC11621018
ArticlePDF–3.1M
17.
Image processing tools for petabyte-scale light sheet microscopy data
Xiongtao Ruan, Matthew Mueller, Gaoxiang Liu, Frederik Görlitz, Tian-Ming Fu, Daniel E. Milkie, Joshua L. Lillvis, Alexander Kuhn, Johnny Gan Chong, Jason Li Hong, Chu Yi Aaron Herr, Wilmene Hercule, Marc Nienhaus, Alison N. Killilea, Eric Betzig, Srigokul Upadhyayula
Nat Methods. 2024; 21(12): 2342–2352. Published online 2024 Oct 17. doi: 10.1038/s41592-024-02475-4
PMCID:
PMC11621031
ArticlePDF–13M
18.
Interpretable spatially aware dimension reduction of spatial transcriptomics with STAMP
Chengwei Zhong, Kok Siong Ang, Jinmiao Chen
Nat Methods. 2024; 21(11): 2072–2083. Published online 2024 Oct 15. doi: 10.1038/s41592-024-02463-8
PMCID:
PMC11541207
ArticlePDF–11M
19.
Restoring protein glycosylation with GlycoShape
Callum M. Ives, Ojas Singh, Silvia D’Andrea, Carl A. Fogarty, Aoife M. Harbison, Akash Satheesan, Beatrice Tropea, Elisa Fadda
Nat Methods. 2024; 21(11): 2117–2127. Published online 2024 Oct 14. doi: 10.1038/s41592-024-02464-7
PMCID:
PMC11541215
ArticlePDF–3.9M
20.
Neural space–time model for dynamic multi-shot imaging
Ruiming Cao, Nikita S. Divekar, James K. Nuñez, Srigokul Upadhyayula, Laura Waller
Nat Methods. 2024; 21(12): 2336–2341. Published online 2024 Sep 24. doi: 10.1038/s41592-024-02417-0
PMCID:
PMC11621023
ArticlePDF–11M

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