{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T11:18:16Z","timestamp":1790767096390,"version":"4.1.0"},"reference-count":45,"publisher":"Elsevier BV","issue":"7","license":[{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2021,11,1]],"date-time":"2021-11-01T00:00:00Z","timestamp":1635724800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2021,10,7]],"date-time":"2021-10-07T00:00:00Z","timestamp":1633564800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports Methods"],"published-print":{"date-parts":[[2021,11]]},"DOI":"10.1016\/j.crmeth.2021.100104","type":"journal-article","created":{"date-parts":[[2021,10,27]],"date-time":"2021-10-27T10:45:10Z","timestamp":1635331510000},"page":"100104","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":27,"title":["Multiplexed imaging and automated signal quantification in formalin-fixed paraffin-embedded tissues by ChipCytometry"],"prefix":"10.1016","volume":"1","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2908-8590","authenticated-orcid":false,"given":"Sebastian","family":"Jarosch","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"K\u00f6hlen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rim S.J.","family":"Sarker","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7269-5433","authenticated-orcid":false,"given":"Katja","family":"Steiger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Klaus-Peter","family":"Janssen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arne","family":"Christians","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8193-5577","authenticated-orcid":false,"given":"Christian","family":"Hennig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ernst","family":"Holler","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elvira","family":"D'Ippolito","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8713-093X","authenticated-orcid":false,"given":"Dirk H.","family":"Busch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.crmeth.2021.100104_bib1","doi-asserted-by":"crossref","first-page":"332","DOI":"10.1158\/1078-0432.CCR-18-1851","article-title":"The immunoscore: colon cancer and beyond","volume":"26","author":"Angell","year":"2020","journal-title":"Clin. Cancer Res."},{"key":"10.1016\/j.crmeth.2021.100104_bib2","doi-asserted-by":"crossref","first-page":"436","DOI":"10.1038\/nm.3488","article-title":"Multiplexed ion beam imaging of human breast tumors","volume":"20","author":"Angelo","year":"2014","journal-title":"Nat. Med."},{"key":"10.1016\/j.crmeth.2021.100104_bib3","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1038\/nbt.4314","article-title":"Dimensionality reduction for visualizing single-cell data using UMAP","volume":"37","author":"Becht","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.crmeth.2021.100104_bib4","doi-asserted-by":"crossref","first-page":"2983","DOI":"10.1172\/JCI124618","article-title":"Innate immune cell-epithelial crosstalk during wound repair","volume":"129","author":"Brazil","year":"2019","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.crmeth.2021.100104_bib5","doi-asserted-by":"crossref","first-page":"6545","DOI":"10.4049\/jimmunol.1001867","article-title":"Reduced functional avidity promotes central and effector memory CD4 T\u00a0cell responses to tumor-associated antigens","volume":"185","author":"Caserta","year":"2010","journal-title":"J.\u00a0Immunol."},{"key":"10.1016\/j.crmeth.2021.100104_bib6","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/j.cell.2017.04.016","article-title":"An immune atlas of clear cell renal cell carcinoma","volume":"169","author":"Chevrier","year":"2017","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2021.100104_bib7","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1016\/j.cels.2018.02.010","article-title":"Compensation of signal spillover in suspension and imaging mass cytometry","volume":"6","author":"Chevrier","year":"2018","journal-title":"Cell Syst."},{"key":"10.1016\/j.crmeth.2021.100104_bib8","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1369\/0022155414531549","article-title":"Characterizing and diminishing autofluorescence in formalin-fixed paraffin-embedded human respiratory tissue","volume":"62","author":"Davis","year":"2014","journal-title":"J.\u00a0Histochem. Cytochem."},{"key":"10.1016\/j.crmeth.2021.100104_bib9","doi-asserted-by":"crossref","first-page":"869","DOI":"10.1007\/s00262-014-1581-4","article-title":"Foxp3 expression in T regulatory cells and other cell lineages","volume":"63","author":"Devaud","year":"2014","journal-title":"Cancer Immunol. Immunother."},{"key":"10.1016\/j.crmeth.2021.100104_bib10","doi-asserted-by":"crossref","first-page":"1144","DOI":"10.1038\/nm915","article-title":"CD4+CD25+ regulatory T\u00a0cells preserve graft-versus-tumor activity while inhibiting graft-versus-host disease after bone marrow transplantation","volume":"9","author":"Edinger","year":"2003","journal-title":"Nat. Med."},{"key":"10.1016\/j.crmeth.2021.100104_bib11","doi-asserted-by":"crossref","first-page":"633","DOI":"10.1016\/j.devcel.2009.03.010","article-title":"Notch signaling: the core pathway and its posttranslational regulation","volume":"16","author":"Fortini","year":"2009","journal-title":"Dev. Cell"},{"key":"10.1016\/j.crmeth.2021.100104_bib12","doi-asserted-by":"crossref","first-page":"373","DOI":"10.1080\/10520295.2018.1446101","article-title":"Factors that drive the increasing use of FFPE tissue in basic and translational cancer research","volume":"93","author":"Gaffney","year":"2018","journal-title":"Biotech. Histochem."},{"key":"10.1016\/j.crmeth.2021.100104_bib13","doi-asserted-by":"crossref","first-page":"11982","DOI":"10.1073\/pnas.1300136110","article-title":"Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue","volume":"110","author":"Gerdes","year":"2013","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10.1016\/j.crmeth.2021.100104_bib14","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.2869","article-title":"Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry","volume":"11","author":"Giesen","year":"2014","journal-title":"Nat. Methods"},{"key":"10.1016\/j.crmeth.2021.100104_bib15","doi-asserted-by":"crossref","first-page":"968","DOI":"10.1016\/j.cell.2018.07.010","article-title":"Deep profiling of mouse splenic architecture with CODEX multiplexed imaging","volume":"174","author":"Goltsev","year":"2018","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2021.100104_bib16","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1002\/cyto.a.20668","article-title":"A versatile platform for comprehensive Chip-based explorative cytometry","volume":"75","author":"Hennig","year":"2009","journal-title":"Cytom. Part A"},{"key":"10.1016\/j.crmeth.2021.100104_bib17","doi-asserted-by":"crossref","first-page":"1262","DOI":"10.1002\/eji.202048891","article-title":"Highly multiplexed tissue imaging using repeated oligonucleotide exchange reaction","volume":"51","author":"Kennedy-Darling","year":"2021","journal-title":"Eur. J. Immunol."},{"key":"10.1016\/j.crmeth.2021.100104_bib18","doi-asserted-by":"crossref","first-page":"3077","DOI":"10.1016\/j.celrep.2019.08.050","article-title":"TCR and inflammatory signals tune human MAIT cells to exert specific tissue repair and effector functions","volume":"28","author":"Leng","year":"2019","journal-title":"Cell Rep."},{"key":"10.1016\/j.crmeth.2021.100104_bib19","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1002\/cpch.14","article-title":"Cyclic immunofluorescence (CycIF), a highly multiplexed method for single-cell imaging","volume":"8","author":"Lin","year":"2016","journal-title":"Curr. Protoc. Chem. Biol."},{"key":"10.1016\/j.crmeth.2021.100104_bib20","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms9390","article-title":"Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method","volume":"6","author":"Lin","year":"2015","journal-title":"Nat. Commun."},{"key":"10.1016\/j.crmeth.2021.100104_bib21","doi-asserted-by":"crossref","first-page":"1","DOI":"10.7554\/eLife.31657","article-title":"Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes","volume":"7","author":"Lin","year":"2018","journal-title":"eLife"},{"key":"10.1016\/j.crmeth.2021.100104_bib22","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1007\/s00418-018-1732-3","article-title":"Emerging role of contact-mediated cell communication in tissue development and diseases","volume":"150","author":"Mattes","year":"2018","journal-title":"Histochem. Cell Biol."},{"key":"10.1016\/j.crmeth.2021.100104_bib23","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1038\/s41587-020-0472-9","article-title":"Multiplex digital spatial profiling of proteins and RNA in fixed tissue","volume":"38","author":"Merritt","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.crmeth.2021.100104_bib24","doi-asserted-by":"crossref","first-page":"899","DOI":"10.1016\/j.immuni.2009.03.019","article-title":"Functional delineation and differentiation dynamics of human CD4+ T\u00a0cells expressing the FoxP3 transcription factor","volume":"30","author":"Miyara","year":"2009","journal-title":"Immunity"},{"key":"10.1016\/j.crmeth.2021.100104_bib25","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.humimm.2004.05.016","article-title":"Expression of FOXP3 mRNA is not confined to CD4+CD25+ T regulatory cells in humans","volume":"66","author":"Morgan","year":"2005","journal-title":"Hum. Immunol."},{"key":"10.1016\/j.crmeth.2021.100104_bib26","doi-asserted-by":"crossref","first-page":"24275","DOI":"10.1073\/pnas.1903854116","article-title":"Long-term in\u00a0vivo microscopy of CAR T\u00a0cell dynamics during eradication of CNS lymphoma in mice","volume":"116","author":"Mulazzani","year":"2019","journal-title":"Proc. Natl. Acad. Sci. U S A"},{"key":"10.1016\/j.crmeth.2021.100104_bib45","first-page":"2021","article-title":"writeFCS(fname, DATA, TEXT, OTHER) (https:\/\/www.mathworks.com\/matlabcentral\/fileexchange\/42603-writefcs-fname-data-text-other), MATLAB Central File Exchange","volume":"21","author":"Nedbal","year":"2021","journal-title":"Retrieved October"},{"key":"10.1016\/j.crmeth.2021.100104_bib27","doi-asserted-by":"crossref","first-page":"42","DOI":"10.1309\/AJCPO92DZMUCGEUF","article-title":"To count and how to count, that is the question: interobserver and intraobserver variability among pathologists in lymph node counting","volume":"134","author":"Parkash","year":"2010","journal-title":"Am. J. Clin. Pathol."},{"key":"10.1016\/j.crmeth.2021.100104_bib28","doi-asserted-by":"crossref","first-page":"247","DOI":"10.3390\/cancers11020247","article-title":"State-of-the-art of profiling immune contexture in the era of multiplexed staining and digital analysis to study paraffin tumor tissues","volume":"11","author":"Parra","year":"2019","journal-title":"Cancers (Basel)"},{"key":"10.1016\/j.crmeth.2021.100104_bib29","doi-asserted-by":"crossref","first-page":"100006","DOI":"10.1016\/j.crmeth.2021.100006","article-title":"SeqStain is an efficient method for multiplexed, spatialomic profiling of human and murine tissues","volume":"1","author":"Rajagopalan","year":"2021","journal-title":"Cell Rep. Methods"},{"key":"10.1016\/j.crmeth.2021.100104_bib30","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1038\/ni.3693","article-title":"Social network architecture of human immune cells unveiled by quantitative proteomics","volume":"18","author":"Rieckmann","year":"2017","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.crmeth.2021.100104_bib31","doi-asserted-by":"crossref","first-page":"1080","DOI":"10.1038\/s41587-019-0207-y","article-title":"Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues","volume":"37","author":"Saka","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.crmeth.2021.100104_bib32","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/j.cell.2008.05.009","article-title":"Regulatory T\u00a0cells and immune tolerance","volume":"133","author":"Sakaguchi","year":"2008","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2021.100104_bib44","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/nmeth.2019","article-title":"Fiji: an open-source platform for biological-image analysis","volume":"9","author":"Schindelin","year":"2012","journal-title":"Nat Methods"},{"key":"10.1016\/j.crmeth.2021.100104_bib33","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1369\/jhc.2010.957191","article-title":"Antigen retrieval immunohistochemistry: review and future prospects in research and diagnosis over two decades","volume":"59","author":"Shi","year":"2011","journal-title":"J.\u00a0Histochem. Cytochem."},{"key":"10.1016\/j.crmeth.2021.100104_bib34","doi-asserted-by":"crossref","first-page":"135","DOI":"10.1002\/cac2.12023","article-title":"Overview of multiplex immunohistochemistry\/immunofluorescence techniques in the era of cancer immunotherapy","volume":"40","author":"Tan","year":"2020","journal-title":"Cancer Commun."},{"key":"10.1016\/j.crmeth.2021.100104_bib35","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1038\/nri.2016.36","article-title":"Development and maintenance of intestinal regulatory T\u00a0cells","volume":"16","author":"Tanoue","year":"2016","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.crmeth.2021.100104_bib36","doi-asserted-by":"crossref","first-page":"3493","DOI":"10.1182\/blood.V99.10.3493","article-title":"The infusion of ex\u00a0vivo activated and expanded CD4+CD25+ immune regulatory cells inhibits graft-versus-host disease lethality","volume":"99","author":"Taylor","year":"2002","journal-title":"Blood"},{"key":"10.1016\/j.crmeth.2021.100104_bib37","doi-asserted-by":"crossref","first-page":"FSO244","DOI":"10.4155\/fsoa-2017-0079","article-title":"A preliminary study for the assessment of PD-L1 and PD-L2 on circulating tumor cells by microfluidic-based chipcytometry","volume":"3","author":"Teo","year":"2017","journal-title":"Futur. Sci. OA"},{"key":"10.1016\/j.crmeth.2021.100104_bib38","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci. Rep."},{"key":"10.1016\/j.crmeth.2021.100104_bib39","first-page":"59","article-title":"An improved and cost-effective methodology for the reduction of autofluorescence in direct immunofluorescence studies on formalin-fixed paraffin-embedded tissues","volume":"51","author":"Viegas","year":"2007","journal-title":"Eur. J. Histochem."},{"key":"10.1016\/j.crmeth.2021.100104_bib40","doi-asserted-by":"crossref","first-page":"53","DOI":"10.3389\/fbioe.2019.00053","article-title":"Methods for segmentation and classification of digital microscopy tissue images","volume":"7","author":"Vu","year":"2019","journal-title":"Front. Bioeng. Biotechnol."},{"key":"10.1016\/j.crmeth.2021.100104_bib41","doi-asserted-by":"crossref","first-page":"1330","DOI":"10.1016\/j.cell.2019.03.005","article-title":"A single-cell atlas of the tumor and immune ecosystem of human breast cancer","volume":"177","author":"Wagner","year":"2019","journal-title":"Cell"},{"key":"10.1016\/j.crmeth.2021.100104_bib42","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Wolf","year":"2018","journal-title":"Genome Biol."},{"key":"10.1016\/j.crmeth.2021.100104_bib43","doi-asserted-by":"crossref","first-page":"79","DOI":"10.12688\/wellcomeopenres.12251.1","article-title":"Quenching autofluorescence in tissue immunofluorescence","volume":"2","author":"Yang","year":"2017","journal-title":"Wellcome Open Res."}],"container-title":["Cell Reports Methods"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237521001636?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2667237521001636?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,9,9]],"date-time":"2025-09-09T07:59:16Z","timestamp":1757404756000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2667237521001636"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11]]},"references-count":45,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2021,11]]}},"alternative-id":["S2667237521001636"],"URL":"https:\/\/doi.org\/10.1016\/j.crmeth.2021.100104","relation":{},"ISSN":["2667-2375"],"issn-type":[{"value":"2667-2375","type":"print"}],"subject":[],"published":{"date-parts":[[2021,11]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Multiplexed imaging and automated signal quantification in formalin-fixed paraffin-embedded tissues by ChipCytometry","name":"articletitle","label":"Article Title"},{"value":"Cell Reports Methods","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.crmeth.2021.100104","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2021 The Author(s).","name":"copyright","label":"Copyright"}],"article-number":"100104"}}