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https://www.nature.com/uploads/product/nmeth/rss.gif http://feeds.nature.com/nmeth/rss/current https://www.nature.com/articles/s41592-025-02717-z Nature Methods, Published online: 23 May 2025; doi:10.1038/s41592-025-02717-zNew spatial transcriptomics platforms are letting researchers map the spatial context of gene expression but are often hamstrung by confounding cell segmentation errors. Computational methods developed to simulate cells offer a new way to think about the problem.]]> doi:10.1038/s41592-025-02717-z Nature Methods, Published online: 2025-05-23; | doi:10.1038/s41592-025-02717-z 2025-05-23 Nature Methods 10.1038/s41592-025-02717-z https://www.nature.com/articles/s41592-025-02717-z https://www.nature.com/articles/s41592-025-02697-0 Nature Methods, Published online: 22 May 2025; doi:10.1038/s41592-025-02697-0Proseg is a segmentation approach for single-cell spatially resolved transcriptomics data that uses unsupervised probabilistic modeling of the spatial distribution of transcripts to accurately segment cells without the need for multimodal staining.]]> Daniel C. JonesAnna E. ElzAzadeh HadadianpourHeeju RyuDavid R. GlassEvan W. Newell doi:10.1038/s41592-025-02697-0 Nature Methods, Published online: 2025-05-22; | doi:10.1038/s41592-025-02697-0 2025-05-22 Nature Methods 10.1038/s41592-025-02697-0 https://www.nature.com/articles/s41592-025-02697-0 https://www.nature.com/articles/s41592-025-02695-2 Nature Methods, Published online: 19 May 2025; doi:10.1038/s41592-025-02695-2Bredt’s rule-inspired, bridged bicycle-strengthened fluorescent dyes resist both photobleaching and photoblueing, offering a powerful new toolkit for super-resolution fluorescence microscopy. This innovative design overcomes longstanding limitations associated with classical fluorescent dyes, enabling exceptional brightness and photostability — critical for capturing comprehensive spatial and temporal information over extended imaging sessions.]]> Frederik BrøndstedLei G. Wang doi:10.1038/s41592-025-02695-2 Nature Methods, Published online: 2025-05-19; | doi:10.1038/s41592-025-02695-2 2025-05-19 Nature Methods 10.1038/s41592-025-02695-2 https://www.nature.com/articles/s41592-025-02695-2 https://www.nature.com/articles/s41592-025-02693-4 Nature Methods, Published online: 19 May 2025; doi:10.1038/s41592-025-02693-4A suite of bridged rhodamine dyes (BriDyes) offers excellent brightness, solubility, photostability, and tunable cell permeability along with resistance to photoblueing, making them exceptional all-purpose dyes for fluorescence biomaging.]]> Junwei ZhangKecheng ZhangKui WangBo WangSiyan ZhuHongping QianYumiao MaMengling ZhangTianyan LiuPeng ChenYuan ShenYunzhe FuShilin FangXinxin ZhangPeng ZouWulan DengYu MuZhixing Chen doi:10.1038/s41592-025-02693-4 Nature Methods, Published online: 2025-05-19; | doi:10.1038/s41592-025-02693-4 2025-05-19 Nature Methods 10.1038/s41592-025-02693-4 https://www.nature.com/articles/s41592-025-02693-4 https://www.nature.com/articles/s41592-025-02692-5 Nature Methods, Published online: 19 May 2025; doi:10.1038/s41592-025-02692-5ALI is an approach for analyzing voltage imaging data that is inspired by algorithms used in super-resolution microscopy. It allows resolving the activity of single neurons in densely labeled populations in scattering conditions.]]> Tsai-Wen ChenXian-Bin HuangSarah E. PlutkisKatie L. HollandLuke D. LavisBei-Jung Lin doi:10.1038/s41592-025-02692-5 Nature Methods, Published online: 2025-05-19; | doi:10.1038/s41592-025-02692-5 2025-05-19 Nature Methods 10.1038/s41592-025-02692-5 https://www.nature.com/articles/s41592-025-02692-5 https://www.nature.com/articles/s41592-025-02701-7 Nature Methods, Published online: 15 May 2025; doi:10.1038/s41592-025-02701-7Vclust generates fast and accurate estimation of average nucleotide identity for viral genomes, scaling clustering to millions of genomes.]]> Andrzej ZielezinskiAdam GudyśJakub BarylskiKrzysztof SiminskiPiotr RozwalakBas E. DutilhSebastian Deorowicz doi:10.1038/s41592-025-02701-7 Nature Methods, Published online: 2025-05-15; | doi:10.1038/s41592-025-02701-7 2025-05-15 Nature Methods 10.1038/s41592-025-02701-7 https://www.nature.com/articles/s41592-025-02701-7 https://www.nature.com/articles/s41592-025-02685-4 Nature Methods, Published online: 14 May 2025; doi:10.1038/s41592-025-02685-4A universal AI-powered pipeline for fast, precise and plug-and-play image analysis of diverse 3D cellular structures across multiple imaging resolutions.]]> Hui Ting OngEsra KaratasTitouan PoquillonGianluca GrenciAlessandro FurlanFlorian DilasserSaburnisha Binte Mohamad RaffiDamien BlancElise DrimaracciDimitri MikecGaetan GalisotBlake A. JohnsonAlbert Zou LiuCora ThielOliver UllrichAudrey VincentVictor RacineAnne Beghin doi:10.1038/s41592-025-02685-4 Nature Methods, Published online: 2025-05-14; | doi:10.1038/s41592-025-02685-4 2025-05-14 Nature Methods 10.1038/s41592-025-02685-4 https://www.nature.com/articles/s41592-025-02685-4 https://www.nature.com/articles/s41592-025-02715-1 Nature Methods, Published online: 13 May 2025; doi:10.1038/s41592-025-02715-1Unraveling the black box in neural signal analysis]]> Nina Vogt doi:10.1038/s41592-025-02715-1 Nature Methods, Published online: 2025-05-13; | doi:10.1038/s41592-025-02715-1 2025-05-13 Nature Methods 10.1038/s41592-025-02715-1 https://www.nature.com/articles/s41592-025-02715-1