{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,9]],"date-time":"2026-01-09T22:24:53Z","timestamp":1767997493648,"version":"3.49.0"},"reference-count":37,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T00:00:00Z","timestamp":1684713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Major Scientific Instrument and Equipment Development Project of NSFC","award":["81827901"],"award-info":[{"award-number":["81827901"]}]},{"name":"Strategic Priority Research Program of the Chinese Academy of Sciences","award":["XDB38030100"],"award-info":[{"award-number":["XDB38030100"]}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2021YFF0703702"],"award-info":[{"award-number":["2021YFF0703702"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2018YFC2000205"],"award-info":[{"award-number":["2018YFC2000205"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012166","name":"National Key R&D Program of China","doi-asserted-by":"publisher","award":["2020YFC2005003"],"award-info":[{"award-number":["2020YFC2005003"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Phase II External Project of Ningbo Institute of Life and Health Industry of University of Chinese Academy of Sciences","award":["2020YJY0217"],"award-info":[{"award-number":["2020YJY0217"]}]},{"name":"Shandong Academician Workstation Program"},{"name":"Shanghai Municipal Science and Technology"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,5]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Understanding the relationship between fine-scale spatial organization and biological function necessitates a tool that effectively combines spatial positions, morphological information, and spatial transcriptomics (ST) data. We introduce the Spatial Multimodal Data Browser (SMDB, https:\/\/www.biosino.org\/smdb), a robust visualization web service for interactively exploring ST data. By integrating multimodal data, such as hematoxylin and eosin (H&amp;E) images, gene expression-based molecular clusters, and more, SMDB facilitates the analysis of tissue composition through the dissociation of two-dimensional (2D) sections and the identification of gene expression-profiled boundaries. In a digital three-dimensional (3D) space, SMDB allows researchers to reconstruct morphology visualizations based on manually filtered spots or expand anatomical structures using high-resolution molecular subtypes. To enhance user experience, it offers customizable workspaces for interactive exploration of ST spots in tissues, providing features like smooth zooming, panning, 360-degree rotation in 3D and adjustable spot scaling. SMDB is particularly valuable in neuroscience and spatial histology studies, as it incorporates Allen's mouse brain anatomy atlas for reference in morphological research. This powerful tool provides a comprehensive and efficient solution for examining the intricate relationships between spatial morphology, and biological function in various tissues.<\/jats:p>","DOI":"10.1093\/nar\/gkad413","type":"journal-article","created":{"date-parts":[[2023,5,22]],"date-time":"2023-05-22T19:32:11Z","timestamp":1684783931000},"page":"W553-W559","source":"Crossref","is-referenced-by-count":9,"title":["SMDB:\u00a0a Spatial Multimodal Data Browser"],"prefix":"10.1093","volume":"51","author":[{"given":"Ruifang","family":"Cao","sequence":"first","affiliation":[{"name":"National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science , Shanghai \u00a0200031, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunchao","family":"Ling","sequence":"additional","affiliation":[{"name":"National Genomics Data 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China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yixue","family":"Li","sequence":"additional","affiliation":[{"name":"National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science , Shanghai \u00a0200031, China"},{"name":"Guangzhou Laboratory , Guangzhou \u00a0510005, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8827-7546","authenticated-orcid":false,"given":"Guoqing","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Genomics Data Center& Bio-Med Big Data Center, CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Science , Shanghai \u00a0200031, 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