{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,7]],"date-time":"2026-04-07T18:17:46Z","timestamp":1775585866407,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"10","license":[{"start":{"date-parts":[[2020,2,12]],"date-time":"2020-02-12T00:00:00Z","timestamp":1581465600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"European Union\u2019s Horizon 2020 programme","award":["N\u00ba634402"],"award-info":[{"award-number":["N\u00ba634402"]}]},{"name":"European Union\u2019s Horizon 2020 programme","award":["N\u00ba777222"],"award-info":[{"award-number":["N\u00ba777222"]}]},{"DOI":"10.13039\/501100002261","name":"Russian Foundation for Basic Research","doi-asserted-by":"publisher","award":["18-54-74005"],"award-info":[{"award-number":["18-54-74005"]}],"id":[{"id":"10.13039\/501100002261","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Research Council Consolidator"},{"name":"METACELL","award":["N\u00ba773089"],"award-info":[{"award-number":["N\u00ba773089"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Imaging mass spectrometry (imaging MS) is a prominent technique for capturing distributions of molecules in tissue sections. Various computational methods for imaging MS rely on quantifying spatial correlations between ion images, referred to as co-localization. However, no comprehensive evaluation of co-localization measures has ever been performed; this leads to arbitrary choices and hinders method development.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We present ColocML, a machine learning approach addressing this gap. With the help of 42 imaging MS experts from nine laboratories, we created a gold standard of 2210 pairs of ion images ranked by their co-localization. We evaluated existing co-localization measures and developed novel measures using term frequency\u2013inverse document frequency and deep neural networks. The semi-supervised deep learning Pi model and the cosine score applied after median thresholding performed the best (Spearman 0.797 and 0.794 with expert rankings, respectively). We illustrate these measures by inferring co-localization properties of 10\u00a0273 molecules from 3685 public METASPACE datasets.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>https:\/\/github.com\/metaspace2020\/coloc.<\/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\/btaa085","type":"journal-article","created":{"date-parts":[[2020,2,5]],"date-time":"2020-02-05T04:31:53Z","timestamp":1580877113000},"page":"3215-3224","source":"Crossref","is-referenced-by-count":43,"title":["ColocML: machine learning quantifies co-localization between mass spectrometry images"],"prefix":"10.1093","volume":"36","author":[{"given":"Katja","family":"Ovchinnikova","sequence":"first","affiliation":[{"name":"Structural and Computational Biology Unit , , Heidelberg, Germany"},{"name":"European Molecular Biology Laboratory , , Heidelberg, Germany"}]},{"given":"Lachlan","family":"Stuart","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit , , Heidelberg, Germany"},{"name":"European Molecular Biology Laboratory , , Heidelberg, Germany"}]},{"given":"Alexander","family":"Rakhlin","sequence":"additional","affiliation":[{"name":"Neuromation OU , Tallinn, Estonia"}]},{"given":"Sergey","family":"Nikolenko","sequence":"additional","affiliation":[{"name":"National Research Institute Higher School of Economics"},{"name":"Steklov Institute of Mathematics at St. Petersburg , St. Petersburg, Russia"}]},{"given":"Theodore","family":"Alexandrov","sequence":"additional","affiliation":[{"name":"Structural and Computational Biology Unit , , Heidelberg, Germany"},{"name":"European Molecular Biology Laboratory , , Heidelberg, Germany"},{"name":"Metabolomics Core Facility, European Molecular Biology Laboratory , Heidelberg, Germany"},{"name":"Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,2,12]]},"reference":[{"key":"2023013111512883600_btaa085-B1","doi-asserted-by":"crossref","first-page":"jcs211847","DOI":"10.1242\/jcs.211847","article-title":"Image co-localization\u2014co-occurrence versus correlation","volume":"131","author":"Aaron","year":"2018","journal-title":"J. Cell Sci"},{"key":"2023013111512883600_btaa085-B2","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2105-13-S16-S11","article-title":"MALDI imaging mass spectrometry: statistical data analysis and current computational challenges","volume":"13","author":"Alexandrov","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2023013111512883600_btaa085-B3","doi-asserted-by":"crossref","first-page":"6535","DOI":"10.1021\/pr100734z","article-title":"Spatial segmentation of imaging mass spectrometry data with edge-preserving image denoising and clustering","volume":"9","author":"Alexandrov","year":"2010","journal-title":"J. Proteome Res"},{"key":"2023013111512883600_btaa085-B4","doi-asserted-by":"crossref","first-page":"11189","DOI":"10.1021\/ac401420z","article-title":"Analysis and interpretation of imaging mass spectrometry data by clustering mass-to-charge images according to their spatial similarity","volume":"85","author":"Alexandrov","year":"2013","journal-title":"Anal. Chem"},{"key":"2023013111512883600_btaa085-B5","author":"Alexandrov","year":"2019"},{"key":"2023013111512883600_btaa085-B6","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1021\/acs.analchem.7b04733","article-title":"Mass spectrometry imaging: a review of emerging advancements and future insights","volume":"90","author":"Buchberger","year":"2018","journal-title":"Anal. Chem"},{"key":"2023013111512883600_btaa085-B7","first-page":"785","author":"Chen","year":"2016"},{"key":"2023013111512883600_btaa085-B8","first-page":"1800","author":"Chollet","year":"2017"},{"key":"2023013111512883600_btaa085-B9","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1038\/nmeth.4546","article-title":"Mass spectrometry imaging takes off","volume":"15","author":"Doerr","year":"2018","journal-title":"Nat. Methods"},{"key":"2023013111512883600_btaa085-B10","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1038\/nmeth.4513","article-title":"Mass spectrometry imaging goes three dimensional","volume":"14","author":"Dreisewerd","year":"2017","journal-title":"Nat. Methods"},{"key":"2023013111512883600_btaa085-B11","doi-asserted-by":"crossref","first-page":"2467","DOI":"10.1007\/s13361-018-2073-0","article-title":"Evaluation of digital image recognition methods for mass spectrometry imaging data analysis","volume":"29","author":"Ekel\u00f6f","year":"2018","journal-title":"J. Am. Soc. Mass Spectrom"},{"key":"2023013111512883600_btaa085-B12","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1109\/TASSP.1979.1163188","article-title":"A fast two-dimensional median filtering algorithm","volume":"27","author":"Huang","year":"1979","journal-title":"IEEE Trans. Acoust. Speech Signal Process"},{"key":"2023013111512883600_btaa085-B13","first-page":"604","author":"Kaddi","year":"2011"},{"key":"2023013111512883600_btaa085-B14","author":"Laine","year":"2016"},{"key":"2023013111512883600_btaa085-B15","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9781139924801","volume-title":"Mining of Massive Datasets","author":"Leskovec","year":"2014"},{"key":"2023013111512883600_btaa085-B16","doi-asserted-by":"crossref","first-page":"6118","DOI":"10.1021\/ac051081q","article-title":"Spatial and spectral correlations in MALDI mass spectrometry images by clustering and multivariate analysis","volume":"77","author":"McCombie","year":"2005","journal-title":"Anal. Chem"},{"key":"2023013111512883600_btaa085-B17","doi-asserted-by":"crossref","first-page":"3619","DOI":"10.1021\/pr800214d","article-title":"Mass spectrometry image correlation: quantifying colocalization","volume":"7","author":"McDonnell","year":"2008","journal-title":"J. Proteome Res"},{"key":"2023013111512883600_btaa085-B18","author":"McInnes","year":"2018"},{"key":"2023013111512883600_btaa085-B19","author":"Ovchinnikova","year":"2019"},{"key":"2023013111512883600_btaa085-B20","doi-asserted-by":"crossref","first-page":"i375","DOI":"10.1093\/bioinformatics\/btv266","article-title":"Using collective expert judge-ments to evaluate quality measures of mass spectrometry images","volume":"31","author":"Palmer","year":"2015","journal-title":"Bioinformatics"},{"key":"2023013111512883600_btaa085-B21","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nmeth.4072","article-title":"FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry","volume":"14","author":"Palmer","year":"2017","journal-title":"Nat. Methods"},{"key":"2023013111512883600_btaa085-B22","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/j.copbio.2018.08.003","article-title":"Advanced MALDI mass spectrometry imaging in pharmaceutical research and drug development","volume":"55","author":"Schulz","year":"2019","journal-title":"Curr. Opin. Biotechnol"},{"key":"2023013111512883600_btaa085-B23","doi-asserted-by":"crossref","first-page":"2690","DOI":"10.1039\/C7AN00565B","article-title":"Mass spectrometry imaging for clinical research\u2014latest developments, applications, and current limitations","volume":"142","author":"Vaysse","year":"2017","journal-title":"Analyst"},{"key":"2023013111512883600_btaa085-B24","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1109\/TIP.2003.819861","article-title":"Image quality assessment: from error visibility to structural similarity","volume":"13","author":"Wang","year":"2004","journal-title":"IEEE Trans. Image Process"},{"key":"2023013111512883600_btaa085-B25","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1002\/jms.1876","article-title":"The evolving field of imaging mass spectrometry and its impact on future biological research","volume":"46","author":"Watrous","year":"2011","journal-title":"J. Mass Spectrom"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btaa085\/32742518\/btaa085.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/10\/3215\/48991209\/bioinformatics_36_10_3215.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/36\/10\/3215\/48991209\/bioinformatics_36_10_3215.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,31]],"date-time":"2023-01-31T20:59:23Z","timestamp":1675198763000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/36\/10\/3215\/5734647"}},"subtitle":[],"editor":[{"given":"Alfonso","family":"Valencia","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2020,2,12]]},"references-count":25,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2020,5,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btaa085","relation":{},"ISSN":["1367-4803","1367-4811"],"issn-type":[{"value":"1367-4803","type":"print"},{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2020,5,15]]},"published":{"date-parts":[[2020,2,12]]}}}