Nature Methods offers a unique interdisciplinary forum for the publication of novel methods. Nature Methods focuses on the life sciences, combining practical, technique-driven subject matter with rigorous peer-review standards to ensure that readers are consistently presented with only the most valuable and highest quality methodological research. The journal offers its readers primary research papers as well as an array of opinions, reviews and short journalistic pieces to provide busy researchers with a broad, yet easily absorbed perspective of important methodological developments in the life sciences. http://feeds.nature.com/nmeth/rss/current Nature Publishing Group en © 2026 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. Nature Methods © 2026 Macmillan Publishers Limited, part of Springer Nature. All rights reserved. permissions@nature.com https://www.nature.com/uploads/product/nmeth/rss.gif http://feeds.nature.com/nmeth/rss/current https://www.nature.com/articles/s41592-026-03214-7 Nature Methods, Published online: 28 August 2026; doi:10.1038/s41592-026-03214-7

In this Comment, we direct attention to initial efforts to establish a high-quality databank of atomic force microscopy (AFM) data: bioAFM-DB. We outline the state of this endeavor, its challenges, and potential courses of action.]]> Jean-Luc PellequerSebastian AguayoAndrea AlessandriniDavid AlsteensToshio AndoAudrey BeaussartMichael BettonTimo BetzKerstin G. BlankSimone BovioClément CampilloClaudio CanaleAlexander X. Cartagena-RiveraFilomena A. CarvalhoIgnacio CasusoGuillaume CharrasMarti ChecaLiam CollinsAdai ColomLuca CostaEtienne DagueTanya E. S. DahmsPedro Jose de PabloAlexandra DelvalléeSimone DinarelliLorna DouganYves F. DufrêneAndra C. DumitruYuri M. EfremovSofiane El-Kirat-ChatelPaolo FacciGeorg E. FantnerAmir Farokh PayamCécile FeuillieCristina FlorsNancy FordeCécile Formosa-DagueGregory FranciusClemens M. FranzKristian FranzeRicardo GarciaSergi Garcia-ManyesNúria GavaraMarina I. GiannottiMarco GirasoleMartin GutholdGeorge R. HeathCéline HeuPeter HinterdorferJamie K. HobbsBart W. HoogenboomSébastien JanelMiklós KellermayerPetr KlapetekNoriyuki KoderaMelanie KoehlerFrank LafontGuillaume LamourJessem LandoulsiValérie M. LaurentPhilippe LeclèreMalgorzata LekkaHongbin LiGiovanni LongoArin MarchesiMarion Mathelié-GuinletGerald A. MeiningerIoanna MelaPierre-Emmanuel MilhietRuben Millan-SolsonaTea Mišić RadićMichaël MolinariFernando Moreno-HerreroMichael A. NashOlivier NoëlYoo Jin OhLaia Pasquina-LemoncheShivprasad PatilPatricia PedrazAna Paula PêgoThomas T. PerkinsMartin PeslTri Thanh PhamLaura PicasAlessandro PodestàJohannes PreinerJan PřibylRoger ProkschPierre-Henri PuechAlice L. B. PyneManfred RadmacherLorena Redondo-MorataFelix RicoWouter H. RoosRobert RosNuno C. SantosUgis SarkansTilman E. SchäfferHermann SchillersZhifeng ShaoDelphine SicardAdam Cohen SimonsenIgor SokolovSusana R. SousaBjørn T. StokkeAndreas StylianouMarek SzymonskiFlorence TamaNeil H. ThomsonTakayuki UchihashiMassimo VassalliClaude VerdierAnthony VialVéronique ViéTomaso ZambelliRenato ZenobiPeng ZhengClaire Valotteau doi:10.1038/s41592-026-03214-7 Nature Methods, Published online: 2026-08-28; | doi:10.1038/s41592-026-03214-7 2026-08-28 Nature Methods 10.1038/s41592-026-03214-7 https://www.nature.com/articles/s41592-026-03214-7 https://www.nature.com/articles/s41592-026-03181-z Nature Methods, Published online: 27 August 2026; doi:10.1038/s41592-026-03181-z

REDCAT is a multimodal, all-optical platform that maps metabolic activity alongside cell identity in intact tissues at single-cell and subcellular resolution. By integrating Raman imaging, autofluorescence and high-plex immunofluorescence, REDCAT has resolved metabolic features in normal lymph nodes, uncovered lipid-redox remodeling in lymphoma, and exposed intratumoral heterogeneity, suggesting a use in functional histopathology.]]> doi:10.1038/s41592-026-03181-z Nature Methods, Published online: 2026-08-27; | doi:10.1038/s41592-026-03181-z 2026-08-27 Nature Methods 10.1038/s41592-026-03181-z https://www.nature.com/articles/s41592-026-03181-z https://www.nature.com/articles/s41592-026-03180-0 Nature Methods, Published online: 27 August 2026; doi:10.1038/s41592-026-03180-0

Raman Enhanced Delineation of Cell Atlases in Tissues (REDCAT) integrates stimulated Raman scattering microscopy and high-plex immunofluorescence to profile single-cell proteins, lipids, nuclear metabolites and redox metabolism in tissue.]]> Yajuan LiZhaojun ZhangArchibald EnninfulNegin FarzadPresha RajbhandariHua TianJungmin NamXiaoyu QinJorge VillazonAnthony A. FungHongje JangZhiliang BaiNancy R. ZhangBrent R. StockwellRong FanMina L. XuZongming MaLingyan Shi doi:10.1038/s41592-026-03180-0 Nature Methods, Published online: 2026-08-27; | doi:10.1038/s41592-026-03180-0 2026-08-27 Nature Methods 10.1038/s41592-026-03180-0 https://www.nature.com/articles/s41592-026-03180-0 https://www.nature.com/articles/s41592-026-03238-z Nature Methods, Published online: 26 August 2026; doi:10.1038/s41592-026-03238-z

Author Correction: OrthoFinder: improved phylogenetic orthology inference with enhanced accuracy and scalability]]> David M. EmmsYi LiuLaurence BelcherJonathan HolmesSteven Kelly doi:10.1038/s41592-026-03238-z Nature Methods, Published online: 2026-08-26; | doi:10.1038/s41592-026-03238-z 2026-08-26 Nature Methods 10.1038/s41592-026-03238-z https://www.nature.com/articles/s41592-026-03238-z https://www.nature.com/articles/s41592-026-03193-9 Nature Methods, Published online: 24 August 2026; doi:10.1038/s41592-026-03193-9

Benchmarking computational tools for cutting-edge technologies such as spatially resolved transcriptomics is challenging owing to the lack of reproducibility, of data and of evaluation strategies that are faithful to multiscale spatial biology. However, we found that complementing computational consensus strategies with feedback from histology and cell biology experts circumvents these limitations to accelerate biological discovery.]]> doi:10.1038/s41592-026-03193-9 Nature Methods, Published online: 2026-08-24; | doi:10.1038/s41592-026-03193-9 2026-08-24 Nature Methods 10.1038/s41592-026-03193-9 https://www.nature.com/articles/s41592-026-03193-9 https://www.nature.com/articles/s41592-026-03194-8 Nature Methods, Published online: 24 August 2026; doi:10.1038/s41592-026-03194-8

Benchmarking spatially aware clustering is challenging. SACCELERATOR is an open-source, extensible framework that formalizes expert-guided spatial clustering analysis.]]> Jieran SunKirti BihariePeiying CaiNiklas Müller-BötticherPaul KiesslingMeghan A. TurnerSøren Helweg DamFlorian HeylSarusan KathirchelvanMartin EmonsSamuel GunzSven TwardziokAmin El-HeliebiMartin ZachariasSøren Helweg DamFadhl AlakwaaShahul AlamMaría CallejaYuzhou ChangThomas ChartrandNigel S. ChouEstella Y. DongMichael FletcherGeorge GavriilidisAlexander KanitzSameesh KherLouis KümmerleFrancesca A. LuongoQirong MaoGiorgia MoranzoniMar M. MorenoAnastasiia OkhtienkoLena PerryLucie PfeiferovaDaryna PikulskaShyam PrabhakarRasool SaghaleyniZaira SeferbekovaVipul SinghalDivya SitaniCharlotte SonesonSebastian TiesmeyerMarco VarroneSiao-Han WongLiya ZaygermanTeresa Zulueta-CoarasaRoland EilsMarcel ReindersRaphael GottardoChristoph KuppeBrian LongAhmed MahfouzMark D. RobinsonNaveed Ishaque doi:10.1038/s41592-026-03194-8 Nature Methods, Published online: 2026-08-24; | doi:10.1038/s41592-026-03194-8 2026-08-24 Nature Methods 10.1038/s41592-026-03194-8 https://www.nature.com/articles/s41592-026-03194-8 https://www.nature.com/articles/s41592-026-03184-w Nature Methods, Published online: 24 August 2026; doi:10.1038/s41592-026-03184-w

MS2 bacteriophage-derived protein shells called ‘nanocrates’ help address the air–water interface-induced artifacts in cryo-EM structure determination by encapsulating target proteins and enabling them to randomly orient at the air–water interface.]]> Matthew C. JenkinsDaija BobeJake D. JohnstonJonah CheungAkira KarasawaChristina M. ZimanyiÖmer DermanciCollin T. McManusM. G. FinnAlex de MarcoMykhailo Kopylov doi:10.1038/s41592-026-03184-w Nature Methods, Published online: 2026-08-24; | doi:10.1038/s41592-026-03184-w 2026-08-24 Nature Methods 10.1038/s41592-026-03184-w https://www.nature.com/articles/s41592-026-03184-w https://www.nature.com/articles/s41592-026-03208-5 Nature Methods, Published online: 21 August 2026; doi:10.1038/s41592-026-03208-5

Cell biologists have long known that mechanical forces, such as tension and compression, influence tissue differentiation. Now, advanced methods are letting them observe and manipulate these forces in real time, in living systems.]]> Caroline Seydel doi:10.1038/s41592-026-03208-5 Nature Methods, Published online: 2026-08-21; | doi:10.1038/s41592-026-03208-5 2026-08-21 Nature Methods 10.1038/s41592-026-03208-5 https://www.nature.com/articles/s41592-026-03208-5