{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T06:29:43Z","timestamp":1788935383212,"version":"build-2803163510"},"reference-count":23,"publisher":"Elsevier BV","issue":"3","license":[{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,9,1]],"date-time":"2024-09-01T00:00:00Z","timestamp":1725148800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,7,5]],"date-time":"2024-07-05T00:00:00Z","timestamp":1720137600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003354","name":"Garnett Passe and Rodney Williams Memorial Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100003354","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008614","name":"Wesley Research Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008614","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["STAR Protocols"],"published-print":{"date-parts":[[2024,9]]},"DOI":"10.1016\/j.xpro.2024.103226","type":"journal-article","created":{"date-parts":[[2024,7,18]],"date-time":"2024-07-18T17:32:20Z","timestamp":1721323940000},"page":"103226","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":26,"title":["Protocol for high-plex, whole-slide imaging of human formalin-fixed paraffin-embedded tissue using PhenoCycler-Fusion"],"prefix":"10.1016","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9875-8914","authenticated-orcid":false,"given":"Meg L.","family":"Donovan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Niyati","family":"Jhaveri","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ning","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bassem Ben","family":"Cheikh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"DeRosa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ritu","family":"Mihani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Naomi","family":"Berrell","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacky Y.","family":"Suen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James","family":"Monkman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John F.","family":"Fraser","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3224-7350","authenticated-orcid":false,"given":"Arutha","family":"Kulasinghe","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.xpro.2024.103226_bib1","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1089\/genbio.2023.0029","article-title":"Mapping the Spatial Proteome of Head and Neck Tumors: Key Immune Mediators and Metabolic Determinants in the Tumor Microenvironment","volume":"2","author":"Jhaveri","year":"2023","journal-title":"GEN Biotechnology"},{"key":"10.1016\/j.xpro.2024.103226_bib2","author":"Akoya Biosciences PhenoCycler-Fusion User"},{"key":"10.1016\/j.xpro.2024.103226_bib3","doi-asserted-by":"crossref","first-page":"3802","DOI":"10.1038\/s41596-021-00556-8","article-title":"CODEX multiplexed tissue imaging with DNA-conjugated antibodies","volume":"16","author":"Black","year":"2021","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.xpro.2024.103226_bib4","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-17204-5","article-title":"QuPath: Open source software for digital pathology image analysis","volume":"7","author":"Bankhead","year":"2017","journal-title":"Sci. Rep."},{"key":"10.1016\/j.xpro.2024.103226_bib5","doi-asserted-by":"crossref","unstructured":"Schmidt U., Weigert M., Broaddus C., Myers G. Cell Detection with Star-Convex Polygons. In: Frangi A.F., Schnabel J.A., Davatzikos C., Alberola-L\u00f3pez C., Fichtinger G., editors. Medical Image Computing and Computer Assisted Intervention \u2013 MICCAI 2018. MICCAI 2018. Lecture Notes in Computer Science, vol 11071. Springer International Publishing; 2018. p. 265\u2013273. Held in Cham.","DOI":"10.1007\/978-3-030-00934-2_30"},{"key":"10.1016\/j.xpro.2024.103226_bib6","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.xpro.2024.103226_bib7","article-title":"Accelerating single-cell genomic analysis with GPUs","author":"Nolet","year":"2022","journal-title":"bioRxiv"},{"key":"10.1016\/j.xpro.2024.103226_bib8","author":"Nirmal"},{"key":"10.1016\/j.xpro.2024.103226_bib9","doi-asserted-by":"crossref","first-page":"239","DOI":"10.1186\/s12967-024-05035-8","article-title":"Spatial insights into immunotherapy response in non-small cell lung cancer (NSCLC) by multiplexed tissue imaging","volume":"22","author":"Monkman","year":"2024","journal-title":"J.\u00a0Transl. Med."},{"key":"10.1016\/j.xpro.2024.103226_bib10","doi-asserted-by":"crossref","DOI":"10.3389\/fimmu.2021.727626","article-title":"Strategies for Accurate Cell Type Identification in CODEX Multiplexed Imaging Data","volume":"12","author":"Hickey","year":"2021","journal-title":"Front. Immunol."},{"key":"10.1016\/j.xpro.2024.103226_bib11","doi-asserted-by":"crossref","first-page":"5233","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.xpro.2024.103226_bib12","article-title":"Umap: Uniform manifold approximation and projection for dimension reduction","author":"McInnes","year":"2018","journal-title":"arXiv"},{"key":"10.1016\/j.xpro.2024.103226_bib13","first-page":"2579","article-title":"Visualizing Data using t-SNE","volume":"9","author":"van der Maaten","year":"2008","journal-title":"J.\u00a0Mach. Learn. Res."},{"key":"10.1016\/j.xpro.2024.103226_bib14","unstructured":"Dicks, S., Philipp, A., Pintar, J., Korten, T., Kumar, A., Virshup, I., and Metzger, P. 2024. scverse\/rapids_singlecell: v0.10.4 (v0.10.4). Zenodo. https:\/\/doi.org\/10.5281\/zenodo.11188193."},{"key":"10.1016\/j.xpro.2024.103226_bib15","doi-asserted-by":"crossref","first-page":"1341","DOI":"10.1016\/j.cell.2020.07.005","article-title":"Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front","volume":"182","author":"Sch\u00fcrch","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.xpro.2024.103226_bib16","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.xpro.2024.103226_bib17","article-title":"Cell Spotter (CSPOT): A machine-learning approach to automated cell spotting and quantification of highly multiplexed tissue images","author":"Nirmal","year":"2023","journal-title":"bioRxiv"},{"key":"10.1016\/j.xpro.2024.103226_bib18","doi-asserted-by":"crossref","first-page":"493","DOI":"10.1038\/nmeth.3863","article-title":"Automated mapping of phenotype space with single-cell data","volume":"13","author":"Samusik","year":"2016","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2024.103226_bib19","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1016\/j.cell.2015.05.047","article-title":"Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis","volume":"162","author":"Levine","year":"2015","journal-title":"Cell"},{"key":"10.1016\/j.xpro.2024.103226_bib20","doi-asserted-by":"crossref","first-page":"311","DOI":"10.1038\/s41592-021-01308-y","article-title":"MCMICRO: a scalable, modular image-processing pipeline for multiplexed\u00a0tissue imaging","volume":"19","author":"Schapiro","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2024.103226_bib21","doi-asserted-by":"crossref","first-page":"759","DOI":"10.1038\/s41592-022-01498-z","article-title":"Identification of cell types in multiplexed in\u00a0situ images by combining protein expression and spatial information using CELESTA","volume":"19","author":"Zhang","year":"2022","journal-title":"Nat. Methods"},{"key":"10.1016\/j.xpro.2024.103226_bib22","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1038\/s41588-024-01664-3","article-title":"BANKSY unifies cell typing and tissue domain segmentation for scalable spatial omics data analysis","volume":"56","author":"Singhal","year":"2024","journal-title":"Nat. Genet."},{"key":"10.1016\/j.xpro.2024.103226_bib23","doi-asserted-by":"crossref","first-page":"3120","DOI":"10.1016\/j.cell.2024.04.013","article-title":"Mapping the cellular biogeography of human bone marrow niches using single-cell transcriptomics and proteomic imaging","volume":"187","author":"Bandyopadhyay","year":"2024","journal-title":"Cell"}],"container-title":["STAR Protocols"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166724003915?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2666166724003915?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T21:27:55Z","timestamp":1762637275000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2666166724003915"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,9]]},"references-count":23,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2024,9]]}},"alternative-id":["S2666166724003915"],"URL":"https:\/\/doi.org\/10.1016\/j.xpro.2024.103226","relation":{},"ISSN":["2666-1667"],"issn-type":[{"value":"2666-1667","type":"print"}],"subject":[],"published":{"date-parts":[[2024,9]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Protocol for high-plex, whole-slide imaging of human formalin-fixed paraffin-embedded tissue using PhenoCycler-Fusion","name":"articletitle","label":"Article Title"},{"value":"STAR Protocols","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.xpro.2024.103226","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Author(s). Published by Elsevier Inc.","name":"copyright","label":"Copyright"}],"article-number":"103226"}}