{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T21:26:37Z","timestamp":1776288397888,"version":"3.50.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T00:00:00Z","timestamp":1729123200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-BIO\/DBI-1759736"],"award-info":[{"award-number":["NSF-BIO\/DBI-1759736"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["NSF-BIO\/DBI-1950412"],"award-info":[{"award-number":["NSF-BIO\/DBI-1950412"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["NIH-NLM-1R01LM013115"],"award-info":[{"award-number":["NIH-NLM-1R01LM013115"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["NIH-NIA-1R01AG078755"],"award-info":[{"award-number":["NIH-NIA-1R01AG078755"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>Joint analysis of mass spectrometry images (MS images) and microscopy images of hematoxylin and eosin (H&amp;E) stained tissues assists pathologists in characterizing the morphological structure of the tissues, and in performing diagnosis. Unfortunately, the analysis is undermined by substantial differences between these modalities in terms of aspect ratios, spatial resolution, number of channels in each image, as well as by large global or small local elastic spatial deformations of one image with respect to the other. Therefore, accurate coregistration of the images is a critical pre-requisite for their joint interpretation. We introduce MSIreg, an open-source R package for coregistration of MSI and H&amp;E images. MSIreg is designed for high-dimensional MSI experiments where each spatial location is represented by thousands of mass features. Unlike most existing coregistration methods, MSIreg implements a landmark free workflow, and quantitative metrics for performance evaluation. We evaluate the performance of MSIreg on six case studies, including coregistration of contiguous tissues with large deformations, as well as simultaneous coregistration of 29 tissue microarray cores.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The R package, installation instructions, and fully reproducible vignettes describing methods and Case Studies are available open-source under the GPL-3.0 license at https:\/\/github.com\/sslakkimsetty\/msireg\/.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae624","type":"journal-article","created":{"date-parts":[[2024,10,17]],"date-time":"2024-10-17T16:51:41Z","timestamp":1729183901000},"source":"Crossref","is-referenced-by-count":6,"title":["<tt>MSIreg<\/tt>: an R package for unsupervised coregistration of mass spectrometry and H&amp;E images"],"prefix":"10.1093","volume":"40","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9552-1121","authenticated-orcid":false,"given":"Sai Srikanth","family":"Lakkimsetty","sequence":"first","affiliation":[{"name":"Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115,","place":["United States"]}]},{"given":"Andreas","family":"Weber","sequence":"additional","affiliation":[{"name":"Institute of Surgical Pathology, University of Freiburg, Faculty of Medicine , Freiburg 79106,","place":["Germany"]},{"name":"Faculty of Biology, University of Freiburg , Freiburg 79104,","place":["Germany"]}]},{"given":"Kylie A","family":"Bemis","sequence":"additional","affiliation":[{"name":"Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115,","place":["United States"]}]},{"given":"Verena","family":"Stehl","sequence":"additional","affiliation":[{"name":"Institute of Pathology, Heinrich Heine University and University Hospital of Duesseldorf , Duesseldorf 40225,","place":["Germany"]}]},{"given":"Peter","family":"Bronsert","sequence":"additional","affiliation":[{"name":"Institute of Surgical Pathology, University of Freiburg, Faculty of Medicine , Freiburg 79106,","place":["Germany"]},{"name":"Tumorbank Comprehensive Cancer Center Freiburg, Medical Center, University of Freiburg , Freiburg 79106,","place":["Germany"]},{"name":"Core Facility for Histopathology and Digital Pathology, Medical Center, University of Freiburg , Freiburg 79106,","place":["Germany"]}]},{"given":"Melanie C","family":"F\u00f6ll","sequence":"additional","affiliation":[{"name":"Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115,","place":["United States"]},{"name":"Institute of Surgical Pathology, University of Freiburg, Faculty of Medicine , Freiburg 79106,","place":["Germany"]},{"name":"German Cancer Consortium and German Cancer Research Center , Heidelberg 69120,","place":["Germany"]}]},{"given":"Olga","family":"Vitek","sequence":"additional","affiliation":[{"name":"Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115,","place":["United States"]}]}],"member":"286","published-online":{"date-parts":[[2024,10,17]]},"reference":[{"key":"2024110121171769800_btae624-B1","doi-asserted-by":"crossref","first-page":"9204","DOI":"10.1021\/ac502170f","article-title":"Automatic generic registration of mass spectrometry imaging data to histology using nonlinear stochastic embedding","volume":"86","author":"Abdelmoula","year":"2014","journal-title":"Anal Chem"},{"key":"2024110121171769800_btae624-B2","doi-asserted-by":"crossref","first-page":"1883","DOI":"10.1038\/s41592-023-02070-z","article-title":"Cardinal v.3: a versatile open-source software for mass spectrometry imaging analysis","volume":"20","author":"Bemis","year":"2023","journal-title":"Nat 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metabolomics","volume":"51","author":"Chen","year":"2023","journal-title":"Drug Metab Dispos"},{"key":"2024110121171769800_btae624-B6","doi-asserted-by":"crossref","first-page":"giab049","DOI":"10.1093\/gigascience\/giab049","article-title":"M2AIA\u2014interactive, fast, and memory-efficient analysis of 2D and 3D multi-modal mass spectrometry imaging data","volume":"10","author":"Cordes","year":"2021","journal-title":"Gigascience"},{"key":"2024110121171769800_btae624-B7","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1186\/s12014-022-09347-z","article-title":"Moving translational mass spectrometry imaging towards transparent and reproducible data analyses: a case study of an urothelial cancer cohort analyzed in the galaxy framework","volume":"19","author":"F\u00f6ll","year":"2022","journal-title":"Clin Proteomics"},{"key":"2024110121171769800_btae624-B8","doi-asserted-by":"crossref","first-page":"W345","DOI":"10.1093\/nar\/gkac247","article-title":"The galaxy platform for 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