biostudies-literatureFerkowicz MJNIDDK NIH HHS661-676https://www.ebi.ac.uk/biostudies/studies/S-EPMC8363780biostudies-literatureUnknown101(5)The advent of personalized medicine has driven the development of novel approaches for obtaining detailed cellular and molecular information from clinical tissue samples. Tissue cytometry is a promising new technique that can be used to enumerate and characterize each cell in a tissue and, unlike flow cytometry and other single-cell techniques, does so in the context of the intact tissue, preserving spatial information that is frequently crucial to understanding a cell's physiology, function, and behavior. However, the wide-scale adoption of tissue cytometry as a research tool has been limited by the fact that published examples utilize specialized techniques that are beyond the capabilities of most laboratories. Here we describe a complete and accessible pipeline, including methods of samLaboratory investigation; a journal of technical methods and pathologyLarge-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline.PMC8363780UH3 DK114923UG3 DK114923K08 DK107864P30 DK079312Mcmahon GWilliams MZhang GCooperman LOtto EJoanes MWright LZhang KWilliams KSanchez FAppelbaum PPasa-Tolic LJefferson NSims-Lucas SSutton TWilson FPKiryluk KKermani ABarwinska DOliver GHJain SKoewler RMoe OLake BD'agati VVillalobos PHe ORosas SCarson JHacohen NGoltsev YSambandam KEadon MSaul JLee SStefanick MParikh SVelickovic DTublin MBalis UMiller TDrager ZUgochukwu UKidney Precision Medicine ProjectFullerton MLecker SHodgin JRandhawa PParikh CWinfree SAshkar TCheng YHPoggio EKelly KHall DShankland SMurugan RSchroeder ADagher PTorrealba JAnderton CTuttle KBoer IBlank KHe CJKhochare SSchaub JDighe AKnight RFerkowicz MKellum JRoberts GEadon MTHerlitz LRosengart MDowd FAzeloglu EStutzke ECDobi DAulisio MO'toole JMenez SNolan GMcclelland RWang NDagher PCAlpers CAlexandrov TKamocka MMElder MMoledina DSutton TAKelly KJPark HLaszik ZPhillips CLRobert TLu CHoover PSharma KBebiak JWaikar SDunn KBarasch JWeng CDunn KWKretzler MGaut JStillman IPinkeney RPalevsky PMooney SFerkowicz MJMehl KHimmelfarb JBarisoni LSedor JShang NSKruth MTroyanskaya OMariani LSteck BMenon RLuciano RRosenberg AIyengar RCampbell TSealfon RBomback ASlack AShpigel AMiegs LVazquez MArdayfio JHayashi LWeins ASabo ARBrown KVijayan AEl-Achkar TMCampbell CStull SfalseLarge-scale, three-dimensional tissue cytometry of the human kidney: a complete and accessible pipeline.The advent of personalized medicine has driven the development of novel approaches for obtaining detailed cellular and molecular information from clinical tissue samples. Tissue cytometry is a promising new technique that can be used to enumerate and characterize each cell in a tissue and, unlike flow cytometry and other single-cell techniques, does so in the context of the intact tissue, preserving spatial information that is frequently crucial to understanding a cell's physiology, function, and behavior. However, the wide-scale adoption of tissue cytometry as a research tool has been limited by the fact that published examples utilize specialized techniques that are beyond the capabilities of most laboratories. Here we describe a complete and accessible pipeline, including methods of sam2021-01-01T00:00:00Z2021 May2025-04-05T10:04:00.08Z2025-04-05T10:04:00.08ZS-EPMC83637803340835010.1038/s41374-020-00518-w