{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T18:17:28Z","timestamp":1790965048123,"version":"4.1.0"},"reference-count":21,"publisher":"Oxford University Press (OUP)","issue":"24","license":[{"start":{"date-parts":[[2020,12,26]],"date-time":"2020-12-26T00:00:00Z","timestamp":1608940800000},"content-version":"vor","delay-in-days":11,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100004410","name":"European Molecular Biology Organization","doi-asserted-by":"publisher","award":["ALTF 1194-2019"],"award-info":[{"award-number":["ALTF 1194-2019"]}],"id":[{"id":"10.13039\/100004410","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000901","name":"JDRF","doi-asserted-by":"publisher","award":["3-PDF-2020-937-A-N"],"award-info":[{"award-number":["3-PDF-2020-937-A-N"]}],"id":[{"id":"10.13039\/100000901","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Institute of Health","award":["DK108132"],"award-info":[{"award-number":["DK108132"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,4,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here, we describe cytomapper, a computational tool written in R, that enables visualization of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its utility, we analysed 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualization of selected cells in corresponding images.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The cytomapper package can be installed via https:\/\/www.bioconductor.org\/packages\/release\/bioc\/html\/cytomapper.html. Code for analysis and further instructions can be found at https:\/\/github.com\/BodenmillerGroup\/cytomapper_publication.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa1061","type":"journal-article","created":{"date-parts":[[2020,12,10]],"date-time":"2020-12-10T16:55:30Z","timestamp":1607619330000},"page":"5706-5708","source":"Crossref","is-referenced-by-count":71,"title":["<i>cytomapper<\/i>\n                    : an R\/Bioconductor package for visualization of highly multiplexed imaging data"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4711-1176","authenticated-orcid":false,"given":"Nils","family":"Eling","sequence":"first","affiliation":[{"name":"Department of Quantitative Biomedicine, University of Zurich , 8057 Zurich, Switzerland"},{"name":"Institute for Molecular Health Sciences , ETH Zurich, 8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3027-8989","authenticated-orcid":false,"given":"Nicolas","family":"Damond","sequence":"additional","affiliation":[{"name":"Department of Quantitative Biomedicine, University of Zurich , 8057 Zurich, Switzerland"},{"name":"Institute for Molecular Health Sciences , ETH Zurich, 8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0319-6064","authenticated-orcid":false,"given":"Tobias","family":"Hoch","sequence":"additional","affiliation":[{"name":"Department of Quantitative Biomedicine, University of Zurich , 8057 Zurich, Switzerland"},{"name":"Institute for Molecular Health Sciences , ETH Zurich, 8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6325-7861","authenticated-orcid":false,"given":"Bernd","family":"Bodenmiller","sequence":"additional","affiliation":[{"name":"Department of Quantitative Biomedicine, University of Zurich , 8057 Zurich, Switzerland"},{"name":"Institute for Molecular Health Sciences , ETH Zurich, 8093 Zurich, Switzerland"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2020,12,26]]},"reference":[{"key":"2023062408132400900_btaa1061-B1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s13059-019-1795-z","article-title":"A comparison of automatic cell identification methods for single-cell RNA sequencing data","volume":"20","author":"Abdelaal","year":"2019","journal-title":"Genome Biol"},{"key":"2023062408132400900_btaa1061-B2","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1038\/s41592-019-0654-x","article-title":"Orchestrating single-cell analysis with Bioconductor","volume":"17","author":"Amezquita","year":"2020","journal-title":"Nat. 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