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NanoSIMS provides chemical images of labeled therapeutics, but assigning these signals to cellular structures requires correlation with electron microscopy (EM). This correlation is commonly performed by manual landmark selection and is therefore time-consuming and operator-dependent. Here, we present an automated computational pipeline for registering chemical and ultrastructural images across multiple spatial scales. The method combines bidirectional RAFT optical-flow estimation, confidence-guided affine fitting, and template matching to locate a NanoSIMS field of view within a larger EM map. A morphology-rich ion channel (for example, 32S) is used to estimate the transformation, which is then applied to molecule-specific channels (for example, 79Br or 15N). Agreement with expert-guided manual registration was evaluated using PSNR and SSIM, and the workflow was applied to several cell and tissue specimens. Applications to labeled oligonucleotide and antibody-based therapeutics demonstrate how the registered images can support organelle-level interpretation of molecular distributions in vitro and in vivo.<\/jats:p>","DOI":"10.1021\/acs.analchem.6c03155","type":"journal-article","created":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T15:01:57Z","timestamp":1789225317000},"page":"28147-28157","source":"Crossref","is-referenced-by-count":0,"title":["Automated Multimodal\nCorrelative Registration for\nOrganelle-Specific Elemental and Isotopic Imaging"],"prefix":"10.1021","volume":"98","author":[{"given":"Chixiang","family":"Lu","sequence":"first","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaiqiang","family":"Zhao","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Di","family":"Cui","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gu","family":"Chen","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Yang","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hui","family":"Yang","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xu","family":"Li","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Murong","family":"Zhao","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kaiyun","family":"Song","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. China, 999077"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mehran","family":"Nikan","sequence":"additional","affiliation":[{"name":"Ionis Pharmaceuticals, Inc , , ,","place":["Carlsbad, California, United States, 92010"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5445-7976","authenticated-orcid":true,"given":"Zhijie","family":"Li","sequence":"additional","affiliation":[{"name":"Shenzhen People\u2019s Hospital , , ,","place":["Shenzhen, P. R. China, 518020"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanchao","family":"Zhao","sequence":"additional","affiliation":[{"name":"Southern Medical University , , ,","place":["Guangzhou, P. R. China, 510900"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinpeng","family":"Cen","sequence":"additional","affiliation":[{"name":"Southern Medical University , , ,","place":["Guangzhou, P. R. China, 510900"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xincheng","family":"Qiu","sequence":"additional","affiliation":[{"name":"China University of Geosciences (Wuhan) , , ,","place":["Wuhan, P. R. China, 430074"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stephen G.","family":"Young","sequence":"additional","affiliation":[{"name":"University of California , , , ,","place":["Los Angeles, California, United States, 90095"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"C. Frank","family":"Bennett","sequence":"additional","affiliation":[{"name":"Ionis Pharmaceuticals, Inc , , ,","place":["Carlsbad, California, United States, 92010"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1783-7806","authenticated-orcid":true,"given":"Punit","family":"Seth","sequence":"additional","affiliation":[{"name":"Ionis Pharmaceuticals, Inc , , ,","place":["Carlsbad, California, United States, 92010"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6850-1723","authenticated-orcid":true,"given":"Kai","family":"Chen","sequence":"additional","affiliation":[{"name":"The University of Western Australia , , ,","place":["Perth, Australia, 6009"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojuan","family":"Qi","sequence":"additional","affiliation":[{"name":"The University of Hong Kong , , Pok Fu Lam , ,","place":["Hong Kong, P. R. 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Opin. Biotechnol."},{"issue":"6","key":"2026092909101947400_cit21","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1038\/nmeth.3400","article-title":"Correlated light\nand electron microscopy: ultrastructure lights up","volume":"12","author":"de Boer","year":"2015","journal-title":"Nat. Methods"},{"key":"2026092909101947400_cit22","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1016\/S0076-6879(08)03617-3","article-title":"Correlative light and electron microscopy","volume":"452","author":"Razi","year":"2009","journal-title":"Methods Enzymol."},{"issue":"9","key":"2026092909101947400_cit23","doi-asserted-by":"publisher","first-page":"1923","DOI":"10.1038\/s41592-025-02794-0","article-title":"CLEM-Reg: an automated point cloud-based\nregistration\nalgorithm for volume correlative light and electron microscopy","volume":"22","author":"Krentzel","year":"2025","journal-title":"Nat. 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Nanobiotechnology"},{"issue":"29","key":"2026092909101947400_cit30","doi-asserted-by":"publisher","first-page":"20221","DOI":"10.1021\/jacs.4c05384","article-title":"Tool\nto Resolve Distortions in Elemental and Isotopic\nImaging","volume":"146","author":"Lu","year":"2024","journal-title":"J. Am. Chem. Soc."},{"key":"2026092909101947400_cit31","doi-asserted-by":"crossref","unstructured":"Teed, Z.; Deng, J.\n          Raft: Recurrent\nall-pairs field\ntransforms for optical flow. 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Natl. Acad. Sci. U. S. A."},{"issue":"23","key":"2026092909101947400_cit36","doi-asserted-by":"publisher","first-page":"4683","DOI":"10.1111\/j.1742-4658.2011.08182.x","article-title":"A guide to taming a toxin--recombinant\nimmunotoxins\nconstructed from Pseudomonas exotoxin A for the treatment of cancer","volume":"278","author":"Weldon","year":"2011","journal-title":"FEBS J."},{"issue":"1","key":"2026092909101947400_cit37","doi-asserted-by":"publisher","first-page":"138","DOI":"10.1128\/iai.15.1.138-144.1977","article-title":"Mechanism\nof action of Pseudomonas\naeruginosa exotoxin Aiadenosine diphosphate-ribosylation of mammalian\nelongation factor 2 in vitro and in vivo","volume":"15","author":"Iglewski","year":"1977","journal-title":"Infect.\nImmun."},{"issue":"3","key":"2026092909101947400_cit38","doi-asserted-by":"publisher","first-page":"475","DOI":"10.1002\/ijc.20371","article-title":"Downregulation\nof the antiapoptotic\nMCL-1 protein and apoptosis in MA-11 breast cancer cells induced by\nan anti-epidermal growth factor receptor-Pseudomonas exotoxin a immunotoxin","volume":"112","author":"Andersson","year":"2004","journal-title":"Int. J. Cancer"},{"issue":"14","key":"2026092909101947400_cit39","doi-asserted-by":"publisher","first-page":"3444","DOI":"10.1128\/MCB.00813-09","article-title":"Pseudomonas exotoxin\nA-mediated apoptosis is Bak dependent and preceded by the degradation\nof Mcl-1","volume":"30","author":"Du","year":"2010","journal-title":"Mol. Cell. Biol."}],"container-title":["Analytical Chemistry"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.analchem.6c03155","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/ancham\/article-pdf\/98\/38\/28147\/68491012\/acs.analchem.6c03155.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/ancham\/article-pdf\/98\/38\/28147\/68491012\/acs.analchem.6c03155.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T13:54:03Z","timestamp":1790690043000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/ancham\/article\/98\/38\/28147\/5428840\/Automated-Multimodal-Correlative-Registration-for"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,12]]},"references-count":39,"journal-issue":{"issue":"38","published-online":{"date-parts":[[2026,9,12]]},"published-print":{"date-parts":[[2026,9,29]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.analchem.6c03155","relation":{},"ISSN":["0003-2700","1520-6882"],"issn-type":[{"value":"0003-2700","type":"print"},{"value":"1520-6882","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,12]]}}}