{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,29]],"date-time":"2026-06-29T22:41:09Z","timestamp":1782772869229,"version":"3.54.5"},"reference-count":5,"publisher":"Oxford University Press (OUP)","issue":"15","license":[{"start":{"date-parts":[[2017,3,30]],"date-time":"2017-03-30T00:00:00Z","timestamp":1490832000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/about_us\/legal\/notices"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2017,8,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>R platform provides some packages that are useful to process mass spectrometry imaging (MSI) data; however, none of them provide an easy to use graphical user interface (GUI). Here, we introduce rMSI, an R package for MSI data analysis focused on providing an efficient way to manage MSI data together with a GUI integrated in R environment. MS data is loaded in rMSI custom format optimized to minimize the memory footprint yet maintaining a fast spectra access. The rMSI GUI is designed for simple and effective data exploration and visualization. Moreover, rMSI is designed to be integrated in the R environment through a library of functions that can be used to share MS data across others R packages. The release of rMSI for R environment establishes a novel and flexible platform for MSI data analysis, completely free and open-source.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and Implementation<\/jats:title>\n                  <jats:p>The code, the documentation, a tutorial and example data are available open-source at: github.com\/prafols\/rMSI.<\/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\/btx182","type":"journal-article","created":{"date-parts":[[2017,3,28]],"date-time":"2017-03-28T14:04:40Z","timestamp":1490709880000},"page":"2427-2428","source":"Crossref","is-referenced-by-count":41,"title":["rMSI: an R package for MS imaging data handling and visualization"],"prefix":"10.1093","volume":"33","author":[{"given":"Pere","family":"R\u00e0fols","sequence":"first","affiliation":[{"name":"Department of Electronic Engineering, Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"S\u00f2nia","family":"Torres","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Noelia","family":"Ram\u00edrez","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Esteban","family":"del Castillo","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, Rovira i Virgili University, IISPV, Tarragona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar","family":"Yanes","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jes\u00fas","family":"Brezmes","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xavier","family":"Correig","sequence":"additional","affiliation":[{"name":"Department of Electronic Engineering, Rovira i Virgili University, IISPV, Tarragona, Spain"},{"name":"Spanish Biomedical Research Centre in Diabetes and Associated Metabolic Disorders (CIBERDEM), Madrid, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2017,3,30]]},"reference":[{"key":"2023063012504769800_btx182-B1","doi-asserted-by":"crossref","first-page":"2418","DOI":"10.1093\/bioinformatics\/btv146","article-title":"Cardinal: an R package for statistical analysis of mass spectrometry-based imaging experiments","volume":"31","author":"Bemis","year":"2015","journal-title":"Bioinformatics"},{"key":"2023063012504769800_btx182-B2","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1002\/prca.201300055","article-title":"Imaging mass spectrometry: a new tool for pathology in a molecular age","volume":"7","author":"Norris","year":"2013","journal-title":"PROTEOMICS Clin. Appl"},{"key":"2023063012504769800_btx182-B3","doi-asserted-by":"crossref","first-page":"9451","DOI":"10.1021\/acs.analchem.6b01643","article-title":"SpectralAnalysis: software for the masses","volume":"88","author":"Race","year":"2016","journal-title":"Anal. Chem"},{"key":"2023063012504769800_btx182-B4","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1007\/s13361-013-0607-z","article-title":"MSiReader: An open-source interface to view and analyze high resolving power MS imaging files on matlab platform","volume":"24","author":"Robichaud","year":"2013","journal-title":"J. Am. Soc. Mass Spectrom"},{"key":"2023063012504769800_btx182-B5","doi-asserted-by":"crossref","first-page":"5106","DOI":"10.1016\/j.jprot.2012.07.026","article-title":"imzML \u2013 a common data format for the flexible exchange and processing of mass spectrometry imaging data","volume":"75","author":"Schramm","year":"2012","journal-title":"J. Proteomics"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2427\/50756578\/bioinformatics_33_15_2427.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/33\/15\/2427\/50756578\/bioinformatics_33_15_2427.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,30]],"date-time":"2023-06-30T12:50:57Z","timestamp":1688129457000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/33\/15\/2427\/3092364"}},"subtitle":[],"editor":[{"given":"Robert","family":"Murphy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,3,30]]},"references-count":5,"journal-issue":{"issue":"15","published-print":{"date-parts":[[2017,8,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btx182","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2017,8,1]]},"published":{"date-parts":[[2017,3,30]]}}}