{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,1]],"date-time":"2026-06-01T12:37:22Z","timestamp":1780317442552,"version":"3.54.1"},"reference-count":39,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T00:00:00Z","timestamp":1681689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12126605"],"award-info":[{"award-number":["12126605"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2021YFA1302500"],"award-info":[{"award-number":["2021YFA1302500"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2019YFA0709501"],"award-info":[{"award-number":["2019YFA0709501"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Key-Area Research and Development of Guangdong Province","award":["2020B1111190001"],"award-info":[{"award-number":["2020B1111190001"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Imaging mass spectrometry (IMS) is one of the powerful tools in spatial metabolomics for obtaining metabolite data and probing the internal microenvironment of organisms. It has dramatically advanced the understanding of the structure of biological tissues and the drug treatment of diseases. However, the complexity of IMS data hinders the further acquisition of biomarkers and the study of certain specific activities of organisms. To this end, we introduce an artificial intelligence tool, SmartGate, to enable automatic peak selection and spatial structure identification in an iterative manner. SmartGate selects discriminative m\/z features from the previous iteration by differential analysis and employs a graph attention autoencoder model to perform spatial clustering for tissue segmentation using the selected features. We applied SmartGate to diverse IMS data at multicellular or subcellular spatial resolutions and compared it with four competing methods to demonstrate its effectiveness. SmartGate can significantly improve the accuracy of spatial segmentation and identify biomarker metabolites based on tissue structure\u2013guided differential analysis. For multiple consecutive IMS data, SmartGate can effectively identify structures with spatial heterogeneity by introducing three-dimensional spatial neighbor information.<\/jats:p>","DOI":"10.1093\/bib\/bbad141","type":"journal-article","created":{"date-parts":[[2023,4,17]],"date-time":"2023-04-17T21:35:25Z","timestamp":1681767325000},"source":"Crossref","is-referenced-by-count":7,"title":["SmartGate is a spatial metabolomics tool for resolving tissue structures"],"prefix":"10.1093","volume":"24","author":[{"given":"Kaixuan","family":"Xiao","sequence":"first","affiliation":[{"name":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190, China"},{"name":"School of Mathematical Sciences\/Sino-Danish College, University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Wang","sequence":"additional","affiliation":[{"name":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190, China"},{"name":"School of Mathematical Sciences\/Sino-Danish College, University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kangning","family":"Dong","sequence":"additional","affiliation":[{"name":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190, China"},{"name":"School of Mathematical Sciences\/Sino-Danish College, University of Chinese Academy of Sciences , Beijing 100049, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shihua","family":"Zhang","sequence":"additional","affiliation":[{"name":"NCMIS, CEMS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences , Beijing 100190, China"},{"name":"School of Mathematical Sciences\/Sino-Danish College, University of Chinese Academy of Sciences , Beijing 100049, China"},{"name":"Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences , Kunming 650223, China"},{"name":"Key Laboratory of Systems Health Science of Zhejiang Province, School of Life Science, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences , Hangzhou, 310024, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,4,17]]},"reference":[{"issue":"1","key":"2023052022214904700_ref1","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1073\/pnas.1808950116","article-title":"Spatially resolved metabolomics to discover tumor-associated metabolic alterations","volume":"116","author":"Sun","year":"2019","journal-title":"Proc Natl Acad Sci"},{"issue":"63","key":"2023052022214904700_ref2","doi-asserted-by":"crossref","first-page":"9801","DOI":"10.1039\/C6CC02387H","article-title":"Maleic anhydride proton sponge as a novel MALDI matrix for the visualization of small 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